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BioPerl <a href="http://en.wikipedia.org/wiki/BioPerl#cite_note-1" style="color: rgb(11, 0, 128); white-space: nowrap; background: none;">[1]</a><a href="http://en.wikipedia.org/wiki/BioPerl#cite_note-2" style="text-decoration: none; color: rgb(11, 0, 128); white-space: nowrap; background: none;">[2]</a> is a collection of <a href="http://en.wikipedia.org/wiki/Perl" title="Perl" style="font-family: sans-serif; font-size: 14px; line-height: 17.9200000762939px; text-decoration: none; color: rgb(11, 0, 128); background: none;">Perl</a> modules that facilitate the development of Perl scripts for <a href="http://en.wikipedia.org/wiki/Bioinformatics" title="Bioinformatics" style="font-family: sans-serif; font-size: 14px; line-height: 17.9200000762939px; text-decoration: none; color: rgb(11, 0, 128); background: none;">bioinformatics</a> applications. It has played an integral role in the <a href="http://en.wikipedia.org/wiki/Human_Genome_Project" title="Human Genome Project" style="font-family: sans-serif; font-size: 14px; line-height: 17.9200000762939px; text-decoration: none; color: rgb(11, 0, 128); background: none;">Human Genome Project</a>.<a href="http://en.wikipedia.org/wiki/BioPerl#cite_note-3" style="text-decoration: none; color: rgb(11, 0, 128); white-space: nowrap; background: none;">[3]</a>
 
<div id="toc" class="toc" style="border: 1px solid rgb(170, 170, 170); padding: 7px; font-size: 13.3000001907349px; display: table; zoom: 1; color: rgb(37, 37, 37); font-family: sans-serif; background-color: rgb(249, 249, 249);">
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<h2 style="color: black; margin: 1em 0px 0.25em; overflow: hidden; padding: 0px; border: none; font-size: 13.3000001907349px; display: inline; line-height: 1.3; background: none;">Contents</h2>
  [<a href="http://en.wikipedia.org/wiki/BioPerl#" id="togglelink" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">hide</a>] </div>
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<li class="toclevel-1 tocsection-1" style="margin-bottom: 0.1em;"><a href="http://en.wikipedia.org/wiki/BioPerl#Background" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">1 Background</a></li>
<li class="toclevel-1 tocsection-2" style="margin-bottom: 0.1em;"><a href="http://en.wikipedia.org/wiki/BioPerl#Features" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">2 Features</a></li>
<li class="toclevel-1 tocsection-3" style="margin-bottom: 0.1em;"><a href="http://en.wikipedia.org/wiki/BioPerl#Usage" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">3 Usage</a></li>
<li class="toclevel-1 tocsection-4" style="margin-bottom: 0.1em;"><a href="http://en.wikipedia.org/wiki/BioPerl#Related_Libraries_in_Other_Programming_Languages" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">4 Related Libraries in Other Programming Languages</a></li>
<li class="toclevel-1 tocsection-5" style="margin-bottom: 0.1em;"><a href="http://en.wikipedia.org/wiki/BioPerl#References" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">5 References</a></li>
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<h2 style="font-weight: normal; margin: 1em 0px 0.25em; overflow: hidden; padding: 0px; border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: rgb(170, 170, 170); font-family: 'Linux Libertine', Georgia, Times, serif; line-height: 1.3; background-image: none; background-attachment: initial; background-size: initial; background-origin: initial; background-clip: initial; background-position: initial; background-repeat: initial;">Background<span class="mw-editsection" style="-webkit-user-select: none; font-size: small; margin-left: 1em; vertical-align: baseline; line-height: 1em; display: inline-block; white-space: nowrap; unicode-bidi: -webkit-isolate; font-family: sans-serif;">[<a href="http://en.wikipedia.org/w/index.php?title=BioPerl&action=edit&section=1" title="Edit section: Background" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">edit</a>]</h2>
BioPerl is an active <a href="http://en.wikipedia.org/wiki/Open_source" title="Open source" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">open source</a> software project supported by the <a href="http://en.wikipedia.org/wiki/Open_Bioinformatics_Foundation" title="Open Bioinformatics Foundation" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">Open Bioinformatics Foundation</a>. The first set of Perl codes of Bioperl was created by <a href="http://en.wikipedia.org/wiki/Tim_Hubbard" title="Tim Hubbard" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">Tim Hubbard</a> and Jong Bhak[<a href="http://en.wikipedia.org/wiki/Wikipedia:Citation_needed" title="Wikipedia:Citation needed" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">citation needed</a>] at <a href="http://en.wikipedia.org/wiki/Medical_Research_Council_(United_Kingdom)" title="Medical Research Council (United Kingdom)" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">MRC</a> Centre Cambridge where the first genome sequencing was carried out by Fred Sanger. MRC Centre was one of the hubs and birth places of modern bioinformatics as it had large amount of DNA sequences and 3D protein structures. The name Bioperl was coined jointly by Jong Bhak and <a href="http://en.wikipedia.org/wiki/Steven_E._Brenner" title="Steven E. Brenner" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">Steve Brenner</a> in a small room of <a href="http://en.wikipedia.org/wiki/Centre_for_Protein_Engineering" title="Centre for Protein Engineering" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">Centre for Protein Engineering</a> (CPE) of MRC Centre where <a href="http://en.wikipedia.org/wiki/Alan_Fersht" title="Alan Fersht" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">Alan Fersht</a> was the director. In that small room, <a href="http://en.wikipedia.org/wiki/Cyrus_Chothia" title="Cyrus Chothia" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">Cyrus Chothia</a> and Tim Hubbard were working with some of their Ph.D. students and colleagues. Tim Hubbard is an expert Perl programmer and he was using th_lib.pl that contained many useful Perl subroutines for bioinformatics. Jong Bhak, being the first Ph.D. student of Tim Hubbard created jong_lib.pl. Jong merged the two Perl subroutine libraries into Bio.pl. One day in 1995, Steve Brenner, a Ph.D. student of Cyrus Chothia visited the room and started to discuss what they would call the perl library after some lengthy (a few months) debate on whether Perl is superior to C for bioinformatics as Steve Brenner had his own C library for bioinformatics. The two Ph.D. students named the net Perl library for biology Bioperl after going through names such as protein perl, protperl, PerlBio, and so on. Steve Brenner organized a Bioperl session in 1995 at <a href="http://en.wikipedia.org/wiki/Intelligent_Systems_for_Molecular_Biology" title="Intelligent Systems for Molecular Biology" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">ISMB</a> Cambridge although it did not really happen. Bioperl had some users in coming months including Georg Fuellen who organized a training course in Germany. Georg's colleagues and students extended the Bioperl much and this was joined later by other people such as Steve Chervitz who was actively developing Perl codes for his yeast genome DB. The major expansion came when another Cambridge student <a href="http://en.wikipedia.org/wiki/Ewan_Birney" title="Ewan Birney" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">Ewan Birney</a> joined the wagon after another lengthy debate on if Perl was superior to C for bioinformatics and Ewan and many other people were very active in developing Bioperl.[<a href="http://en.wikipedia.org/wiki/Wikipedia:Citation_needed" title="Wikipedia:Citation needed" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">citation needed</a>]
The first stable release was on 11 June 2002; the most recent stable (in terms of API) release is 1.6.9 from 14 April 2011. There are also developer releases produced periodically. Version series 1.6.0 is considered to be the most stable (in terms of bugs) version of BioPerl and is recommended for everyday use, but the nightly builds are also extremely stable, and many BioPerl users stay current with those.
In order to take advantage of BioPerl, the user needs a basic understanding of the Perl programming language including an understanding of how to use Perl references, modules, objects and methods.
<h2 style="font-weight: normal; margin: 1em 0px 0.25em; overflow: hidden; padding: 0px; border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: rgb(170, 170, 170); font-family: 'Linux Libertine', Georgia, Times, serif; line-height: 1.3; background-image: none; background-attachment: initial; background-size: initial; background-origin: initial; background-clip: initial; background-position: initial; background-repeat: initial;">Features<span class="mw-editsection" style="-webkit-user-select: none; font-size: small; margin-left: 1em; vertical-align: baseline; line-height: 1em; display: inline-block; white-space: nowrap; unicode-bidi: -webkit-isolate; font-family: sans-serif;">[<a href="http://en.wikipedia.org/w/index.php?title=BioPerl&action=edit&section=2" title="Edit section: Features" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">edit</a>]</h2>
BioPerl provides software modules for many of the typical tasks of bioinformatics programming. These include:
<ul style="line-height: 1.5em; margin: 0.3em 0px 0px 1.6em; padding: 0px; list-style-image: url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%0A%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20version%3D%221.1%22%20width%3D%225%22%20height%3D%2213%22%3E%0A%3Ccircle%20cx%3D%222.5%22%20cy%3D%229.5%22%20r%3D%222.5%22%20fill%3D%22%2300528c%22%2F%3E%0A%3C%2Fsvg%3E%0A); color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px;">
<li style="margin-bottom: 0.1em;">Accessing <a href="http://en.wikipedia.org/wiki/Nucleotide_sequence" title="Nucleotide sequence" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">nucleotide</a> and <a href="http://en.wikipedia.org/wiki/Peptide_sequence" title="Peptide sequence" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">peptide</a> sequence data from local and remote <a href="http://en.wikipedia.org/wiki/Biological_database" title="Biological database" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">databases</a></li>
<li style="margin-bottom: 0.1em;">Transforming <a href="http://en.wikipedia.org/wiki/List_of_file_formats#Biology" title="List of file formats" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">formats</a> of database/ file records</li>
<li style="margin-bottom: 0.1em;">Manipulating individual sequences</li>
<li style="margin-bottom: 0.1em;">Searching for similar sequences</li>
<li style="margin-bottom: 0.1em;">Creating and manipulating <a href="http://en.wikipedia.org/wiki/Sequence_alignment" title="Sequence alignment" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">sequence alignments</a></li>
<li style="margin-bottom: 0.1em;">Searching for <a href="http://en.wikipedia.org/wiki/Gene" title="Gene" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">genes</a> and other structures on <a href="http://en.wikipedia.org/wiki/Genome" title="Genome" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">genomic</a> DNA</li>
<li style="margin-bottom: 0.1em;">Developing machine readable sequence <a href="http://en.wikipedia.org/wiki/Genome_project#Genome_annotation" title="Genome project" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">annotations</a></li>
</ul>
<h2 style="font-weight: normal; margin: 1em 0px 0.25em; overflow: hidden; padding: 0px; border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: rgb(170, 170, 170); font-family: 'Linux Libertine', Georgia, Times, serif; line-height: 1.3; background-image: none; background-attachment: initial; background-size: initial; background-origin: initial; background-clip: initial; background-position: initial; background-repeat: initial;">Usage<span class="mw-editsection" style="-webkit-user-select: none; font-size: small; margin-left: 1em; vertical-align: baseline; line-height: 1em; display: inline-block; white-space: nowrap; unicode-bidi: -webkit-isolate; font-family: sans-serif;">[<a href="http://en.wikipedia.org/w/index.php?title=BioPerl&action=edit&section=3" title="Edit section: Usage" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">edit</a>]</h2>
In addition to being used directly by end-users,<a href="http://en.wikipedia.org/wiki/BioPerl#cite_note-4" style="text-decoration: none; color: rgb(11, 0, 128); white-space: nowrap; background: none;">[4]</a> BioPerl has also provided the base for a wide variety of bioinformatic tools, including <a rel="nofollow" class="external text" href="http://www.bioperl.org/wiki/BioPerl_publications" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">amongst others</a>:
<ul style="line-height: 1.5em; margin: 0.3em 0px 0px 1.6em; padding: 0px; list-style-image: url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%0A%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20version%3D%221.1%22%20width%3D%225%22%20height%3D%2213%22%3E%0A%3Ccircle%20cx%3D%222.5%22%20cy%3D%229.5%22%20r%3D%222.5%22%20fill%3D%22%2300528c%22%2F%3E%0A%3C%2Fsvg%3E%0A); color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px;">
<li style="margin-bottom: 0.1em;">SynBrowse <a href="http://en.wikipedia.org/wiki/BioPerl#cite_note-5" style="text-decoration: none; color: rgb(11, 0, 128); white-space: nowrap; background: none;">[5]</a></li>
<li style="margin-bottom: 0.1em;">GeneComber <a href="http://en.wikipedia.org/wiki/BioPerl#cite_note-6" style="text-decoration: none; color: rgb(11, 0, 128); white-space: nowrap; background: none;">[6]</a></li>
<li style="margin-bottom: 0.1em;">TFBS <a href="http://en.wikipedia.org/wiki/BioPerl#cite_note-7" style="text-decoration: none; color: rgb(11, 0, 128); white-space: nowrap; background: none;">[7]</a></li>
<li style="margin-bottom: 0.1em;">MIMOX <a href="http://en.wikipedia.org/wiki/BioPerl#cite_note-8" style="text-decoration: none; color: rgb(11, 0, 128); white-space: nowrap; background: none;">[8]</a></li>
<li style="margin-bottom: 0.1em;">BioParser <a href="http://en.wikipedia.org/wiki/BioPerl#cite_note-9" style="text-decoration: none; color: rgb(11, 0, 128); white-space: nowrap; background: none;">[9]</a></li>
<li style="margin-bottom: 0.1em;">Degenerate primer design <a href="http://en.wikipedia.org/wiki/BioPerl#cite_note-10" style="text-decoration: none; color: rgb(11, 0, 128); white-space: nowrap; background: none;">[10]</a></li>
<li style="margin-bottom: 0.1em;">Querying the public databases <a href="http://en.wikipedia.org/wiki/BioPerl#cite_note-11" style="text-decoration: none; color: rgb(11, 0, 128); white-space: nowrap; background: none;">[11]</a></li>
<li style="margin-bottom: 0.1em;">Current Comparative Table <a href="http://en.wikipedia.org/wiki/BioPerl#cite_note-12" style="text-decoration: none; color: rgb(11, 0, 128); white-space: nowrap; background: none;">[12]</a></li>
</ul>
New tools and algorithms from external developers are often integrated directly into BioPerl itself:
<ul style="line-height: 1.5em; margin: 0.3em 0px 0px 1.6em; padding: 0px; list-style-image: url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%0A%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20version%3D%221.1%22%20width%3D%225%22%20height%3D%2213%22%3E%0A%3Ccircle%20cx%3D%222.5%22%20cy%3D%229.5%22%20r%3D%222.5%22%20fill%3D%22%2300528c%22%2F%3E%0A%3C%2Fsvg%3E%0A); color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px;">
<li style="margin-bottom: 0.1em;">Dealing with phylogenetic trees and nested taxa <a href="http://en.wikipedia.org/wiki/BioPerl#cite_note-13" style="text-decoration: none; color: rgb(11, 0, 128); white-space: nowrap; background: none;">[13]</a></li>
<li style="margin-bottom: 0.1em;">FPC Web tools <a href="http://en.wikipedia.org/wiki/BioPerl#cite_note-14" style="text-decoration: none; color: rgb(11, 0, 128); white-space: nowrap; background: none;">[14]</a></li>
</ul>
<h2 style="font-weight: normal; margin: 1em 0px 0.25em; overflow: hidden; padding: 0px; border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: rgb(170, 170, 170); font-family: 'Linux Libertine', Georgia, Times, serif; line-height: 1.3; background-image: none; background-attachment: initial; background-size: initial; background-origin: initial; background-clip: initial; background-position: initial; background-repeat: initial;">Related Libraries in Other Programming Languages<span class="mw-editsection" style="-webkit-user-select: none; font-size: small; margin-left: 1em; vertical-align: baseline; line-height: 1em; display: inline-block; white-space: nowrap; unicode-bidi: -webkit-isolate; font-family: sans-serif;">[<a href="http://en.wikipedia.org/w/index.php?title=BioPerl&action=edit&section=4" title="Edit section: Related Libraries in Other Programming Languages" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">edit</a>]</h2>
Several related bioinformatics libraries implemented in other programming languages exist as part of the <a href="http://en.wikipedia.org/wiki/Open_Bioinformatics_Foundation" title="Open Bioinformatics Foundation" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">Open Bioinformatics Foundation</a> including:
<ul style="line-height: 1.5em; margin: 0.3em 0px 0px 1.6em; padding: 0px; list-style-image: url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%0A%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20version%3D%221.1%22%20width%3D%225%22%20height%3D%2213%22%3E%0A%3Ccircle%20cx%3D%222.5%22%20cy%3D%229.5%22%20r%3D%222.5%22%20fill%3D%22%2300528c%22%2F%3E%0A%3C%2Fsvg%3E%0A); color: rgb(37, 37, 37); font-family: sans-serif; font-size: 14px;">
<li style="margin-bottom: 0.1em;"><a href="http://en.wikipedia.org/wiki/Biopython" title="Biopython" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">Biopython</a></li>
<li style="margin-bottom: 0.1em;"><a href="http://en.wikipedia.org/wiki/BioJava" title="BioJava" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">BioJava</a></li>
<li style="margin-bottom: 0.1em;"><a href="http://en.wikipedia.org/wiki/BioRuby" title="BioRuby" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">BioRuby</a></li>
<li style="margin-bottom: 0.1em;"><a href="http://en.wikipedia.org/wiki/BioPHP" title="BioPHP" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">BioPHP</a></li>
<li style="margin-bottom: 0.1em;"><a href="http://en.wikipedia.org/wiki/BioJS" title="BioJS" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">BioJS</a></li>
<li style="margin-bottom: 0.1em;"><a href="http://en.wikipedia.org/wiki/Bioconductor" title="Bioconductor" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">Bioconductor</a></li>
</ul>
<h2 style="font-weight: normal; margin: 1em 0px 0.25em; overflow: hidden; padding: 0px; border-bottom-width: 1px; border-bottom-style: solid; border-bottom-color: rgb(170, 170, 170); font-family: 'Linux Libertine', Georgia, Times, serif; line-height: 1.3; background-image: none; background-attachment: initial; background-size: initial; background-origin: initial; background-clip: initial; background-position: initial; background-repeat: initial;">References<span class="mw-editsection" style="-webkit-user-select: none; font-size: small; margin-left: 1em; vertical-align: baseline; line-height: 1em; display: inline-block; white-space: nowrap; unicode-bidi: -webkit-isolate; font-family: sans-serif;">[<a href="http://en.wikipedia.org/w/index.php?title=BioPerl&action=edit&section=5" title="Edit section: References" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">edit</a>]</h2>
<div class="reflist columns references-column-count references-column-count-2" style="font-size: 12.6000003814697px; margin-bottom: 0.5em; margin-top: 0.3em; color: rgb(37, 37, 37); font-family: sans-serif; -webkit-column-count: 2; list-style-type: decimal;">
<ol class="references" style="line-height: 1.5em; margin: 0px 0px 0.5em 3.2em; padding: 0px; list-style-image: none; font-size: 12.6000003814697px; list-style-type: inherit;">
<li id="cite_note-1" style="margin-bottom: 0.1em; -webkit-column-break-inside: avoid; page-break-inside: avoid;"><a href="http://en.wikipedia.org/wiki/BioPerl#cite_ref-1" style="text-decoration: none; color: rgb(11, 0, 128); background: none;"><span class="cite-accessibility-label" style="top: -99999px; clip: rect(1px 1px 1px 1px); overflow: hidden; position: absolute !important; padding: 0px !important; border: 0px !important; height: 1px !important; width: 1px !important; -webkit-user-select: none;">Jump up^</a> Stajich, J. E.; Block, D.; Boulez, K.; <a href="http://en.wikipedia.org/wiki/Steven_E._Brenner" title="Steven E. Brenner" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">Brenner, S.</a>; Chervitz, S.; Dagdigian, C.; Fuellen, G.; Gilbert, J.; Korf, I.; Lapp, H.; Lehväslaiho, H.; Matsalla, C.; Mungall, C. J.; Osborne, B. I.; Pocock, M. R.; Schattner, P.; Senger, M.; <a href="http://en.wikipedia.org/wiki/Lincoln_Stein" title="Lincoln Stein" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">Stein, L. D.</a>; Stupka, E.; Wilkinson, M. D.; <a href="http://en.wikipedia.org/wiki/Ewan_Birney" title="Ewan Birney" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">Birney, E.</a> (2002). <a rel="nofollow" class="external text" href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC187536" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">"The BioPerl Toolkit: Perl Modules for the Life Sciences"</a>. Genome Research12 (10): 1611–1618. <a href="http://en.wikipedia.org/wiki/Digital_object_identifier" title="Digital object identifier" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">doi</a>:<a rel="nofollow" class="external text" href="http://dx.doi.org/10.1101%2Fgr.361602" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">10.1101/gr.361602</a>. <a href="http://en.wikipedia.org/wiki/PubMed_Central" title="PubMed Central" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">PMC</a> <a rel="nofollow" class="external text" href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC187536" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">187536</a>. <a href="http://en.wikipedia.org/wiki/PubMed_Identifier" title="PubMed Identifier" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">PMID</a> <a rel="nofollow" class="external text" href="http://www.ncbi.nlm.nih.gov/pubmed/12368254" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">12368254</a>. <a class="external text" href="http://en.wikipedia.org/w/index.php?title=Template:Cite_doi/10.1101.2Fgr.361602&action=edit&editintro=Template:Cite_doi/editintro2" style="text-decoration: none; color: rgb(102, 51, 102); padding: 0px !important; background: none !important;">edit</a></li>
<li id="cite_note-2" style="margin-bottom: 0.1em; -webkit-column-break-inside: avoid; page-break-inside: avoid;"><a href="http://en.wikipedia.org/wiki/BioPerl#cite_ref-2" style="text-decoration: none; color: rgb(11, 0, 128); background: none;"><span class="cite-accessibility-label" style="top: -99999px; clip: rect(1px 1px 1px 1px); overflow: hidden; position: absolute !important; padding: 0px !important; border: 0px !important; height: 1px !important; width: 1px !important; -webkit-user-select: none;">Jump up^</a> <a rel="nofollow" class="external free" href="http://www.bioperl.org/wiki/BioPerl_publications" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">http://www.bioperl.org/wiki/BioPerl_publications</a> A complete, up-to-date list of BioPerl references</li>
<li id="cite_note-3" style="margin-bottom: 0.1em; -webkit-column-break-inside: avoid; page-break-inside: avoid;"><a href="http://en.wikipedia.org/wiki/BioPerl#cite_ref-3" style="text-decoration: none; color: rgb(11, 0, 128); background: none;"><span class="cite-accessibility-label" style="top: -99999px; clip: rect(1px 1px 1px 1px); overflow: hidden; position: absolute !important; padding: 0px !important; border: 0px !important; height: 1px !important; width: 1px !important; -webkit-user-select: none;">Jump up^</a> <a href="http://en.wikipedia.org/wiki/Lincoln_Stein" title="Lincoln Stein" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">Lincoln Stein</a> (1996). <a rel="nofollow" class="external text" href="http://www.bioperl.org/wiki/How_Perl_saved_human_genome" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">"How Perl saved the human genome project"</a>. The Perl Journal1 (2). Retrieved 2009-02-25 (Bioperl.org). Check date values in: <code style="font-family: monospace, Courier; color: inherit; border: inherit; border-radius: 2px; padding: inherit; background-color: rgb(249, 249, 249);">|accessdate=</code> (<a href="http://en.wikipedia.org/wiki/Help:CS1_errors#bad_date" title="Help:CS1 errors" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">help</a>)</li>
<li id="cite_note-4" style="margin-bottom: 0.1em; -webkit-column-break-inside: avoid; page-break-inside: avoid;"><a href="http://en.wikipedia.org/wiki/BioPerl#cite_ref-4" style="text-decoration: none; color: rgb(11, 0, 128); background: none;"><span class="cite-accessibility-label" style="top: -99999px; clip: rect(1px 1px 1px 1px); overflow: hidden; position: absolute !important; padding: 0px !important; border: 0px !important; height: 1px !important; width: 1px !important; -webkit-user-select: none;">Jump up^</a> Khaja R, MacDonald J, Zhang J, Scherer S (2006). "Methods for identifying and mapping recent segmental and gene duplications in eukaryotic genomes". Methods Mol Biol 338: 9–20. <a href="http://en.wikipedia.org/wiki/Digital_object_identifier" title="Digital object identifier" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">doi</a>:<a rel="nofollow" class="external text" href="http://dx.doi.org/10.1385%2F1-59745-097-9%3A9" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">10.1385/1-59745-097-9:9</a>. <a href="http://en.wikipedia.org/wiki/International_Standard_Book_Number" title="International Standard Book Number" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">ISBN</a> <a href="http://en.wikipedia.org/wiki/Special:BookSources/1-59745-097-9" title="Special:BookSources/1-59745-097-9" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">1-59745-097-9</a>. <a href="http://en.wikipedia.org/wiki/PubMed_Identifier" title="PubMed Identifier" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">PMID</a> <a rel="nofollow" class="external text" href="http://www.ncbi.nlm.nih.gov/pubmed/16888347" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">16888347</a>.</li>
<li id="cite_note-5" style="margin-bottom: 0.1em; -webkit-column-break-inside: avoid; page-break-inside: avoid;"><a href="http://en.wikipedia.org/wiki/BioPerl#cite_ref-5" style="text-decoration: none; color: rgb(11, 0, 128); background: none;"><span class="cite-accessibility-label" style="top: -99999px; clip: rect(1px 1px 1px 1px); overflow: hidden; position: absolute !important; padding: 0px !important; border: 0px !important; height: 1px !important; width: 1px !important; -webkit-user-select: none;">Jump up^</a> Pan, X.; <a href="http://en.wikipedia.org/wiki/Lincoln_Stein" title="Lincoln Stein" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">Stein, L.</a>; Brendel, V. (2005). "SynBrowse: A synteny browser for comparative sequence analysis". Bioinformatics 21 (17): 3461–3468.<a href="http://en.wikipedia.org/wiki/Digital_object_identifier" title="Digital object identifier" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">doi</a>:<a rel="nofollow" class="external text" href="http://dx.doi.org/10.1093%2Fbioinformatics%2Fbti555" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">10.1093/bioinformatics/bti555</a>. <a href="http://en.wikipedia.org/wiki/PubMed_Identifier" title="PubMed Identifier" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">PMID</a> <a rel="nofollow" class="external text" href="http://www.ncbi.nlm.nih.gov/pubmed/15994196" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">15994196</a>. <a class="external text" href="http://en.wikipedia.org/w/index.php?title=Template:Cite_doi/10.1093.2Fbioinformatics.2Fbti555&action=edit&editintro=Template:Cite_doi/editintro2" style="text-decoration: none; color: rgb(102, 51, 102); padding: 0px !important; background: none !important;">edit</a></li>
<li id="cite_note-6" style="margin-bottom: 0.1em; -webkit-column-break-inside: avoid; page-break-inside: avoid;"><a href="http://en.wikipedia.org/wiki/BioPerl#cite_ref-6" style="text-decoration: none; color: rgb(11, 0, 128); background: none;"><span class="cite-accessibility-label" style="top: -99999px; clip: rect(1px 1px 1px 1px); overflow: hidden; position: absolute !important; padding: 0px !important; border: 0px !important; height: 1px !important; width: 1px !important; -webkit-user-select: none;">Jump up^</a> Shah, S. P.; McVicker, G. P.; MacKworth, A. K.; Rogic, S.; Ouellette, B. F. F. (2003). "GeneComber: Combining outputs of gene prediction programs for improved results".Bioinformatics 19 (10): 1296–1297. <a href="http://en.wikipedia.org/wiki/Digital_object_identifier" title="Digital object identifier" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">doi</a>:<a rel="nofollow" class="external text" href="http://dx.doi.org/10.1093%2Fbioinformatics%2Fbtg139" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">10.1093/bioinformatics/btg139</a>.<a href="http://en.wikipedia.org/wiki/PubMed_Identifier" title="PubMed Identifier" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">PMID</a> <a rel="nofollow" class="external text" href="http://www.ncbi.nlm.nih.gov/pubmed/12835277" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">12835277</a>. <a class="external text" href="http://en.wikipedia.org/w/index.php?title=Template:Cite_doi/10.1093.2Fbioinformatics.2Fbtg139&action=edit&editintro=Template:Cite_doi/editintro2" style="text-decoration: none; color: rgb(102, 51, 102); padding: 0px !important; background: none !important;">edit</a></li>
<li id="cite_note-7" style="margin-bottom: 0.1em; -webkit-column-break-inside: avoid; page-break-inside: avoid;"><a href="http://en.wikipedia.org/wiki/BioPerl#cite_ref-7" style="text-decoration: none; color: rgb(11, 0, 128); background: none;"><span class="cite-accessibility-label" style="top: -99999px; clip: rect(1px 1px 1px 1px); overflow: hidden; position: absolute !important; padding: 0px !important; border: 0px !important; height: 1px !important; width: 1px !important; -webkit-user-select: none;">Jump up^</a> Lenhard, B.; Wasserman, W. W. (2002). "TFBS: Computational framework for transcription factor binding site analysis". Bioinformatics 18 (8): 1135–1136.<a href="http://en.wikipedia.org/wiki/Digital_object_identifier" title="Digital object identifier" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">doi</a>:<a rel="nofollow" class="external text" href="http://dx.doi.org/10.1093%2Fbioinformatics%2F18.8.1135" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">10.1093/bioinformatics/18.8.1135</a>. <a href="http://en.wikipedia.org/wiki/PubMed_Identifier" title="PubMed Identifier" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">PMID</a> <a rel="nofollow" class="external text" href="http://www.ncbi.nlm.nih.gov/pubmed/12176838" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">12176838</a>. <a class="external text" href="http://en.wikipedia.org/w/index.php?title=Template:Cite_doi/10.1093.2Fbioinformatics.2F18.8.1135&action=edit&editintro=Template:Cite_doi/editintro2" style="text-decoration: none; color: rgb(102, 51, 102); padding: 0px !important; background: none !important;">edit</a></li>
<li id="cite_note-8" style="margin-bottom: 0.1em; -webkit-column-break-inside: avoid; page-break-inside: avoid;"><a href="http://en.wikipedia.org/wiki/BioPerl#cite_ref-8" style="text-decoration: none; color: rgb(11, 0, 128); background: none;"><span class="cite-accessibility-label" style="top: -99999px; clip: rect(1px 1px 1px 1px); overflow: hidden; position: absolute !important; padding: 0px !important; border: 0px !important; height: 1px !important; width: 1px !important; -webkit-user-select: none;">Jump up^</a> Huang, J.; Gutteridge, A.; Honda, W.; Kanehisa, M. (2006). <a rel="nofollow" class="external text" href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1618411" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">"MIMOX: A web tool for phage display based epitope mapping"</a>. BMC Bioinformatics 7: 451. <a href="http://en.wikipedia.org/wiki/Digital_object_identifier" title="Digital object identifier" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">doi</a>:<a rel="nofollow" class="external text" href="http://dx.doi.org/10.1186%2F1471-2105-7-451" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">10.1186/1471-2105-7-451</a>. <a href="http://en.wikipedia.org/wiki/PubMed_Central" title="PubMed Central" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">PMC</a> <a rel="nofollow" class="external text" href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1618411" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">1618411</a>. <a href="http://en.wikipedia.org/wiki/PubMed_Identifier" title="PubMed Identifier" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">PMID</a> <a rel="nofollow" class="external text" href="http://www.ncbi.nlm.nih.gov/pubmed/17038191" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">17038191</a>. <a class="external text" href="http://en.wikipedia.org/w/index.php?title=Template:Cite_doi/10.1186.2F1471-2105-7-451&action=edit&editintro=Template:Cite_doi/editintro2" style="text-decoration: none; color: rgb(102, 51, 102); padding: 0px !important; background: none !important;">edit</a></li>
<li id="cite_note-9" style="margin-bottom: 0.1em; -webkit-column-break-inside: avoid; page-break-inside: avoid;"><a href="http://en.wikipedia.org/wiki/BioPerl#cite_ref-9" style="text-decoration: none; color: rgb(11, 0, 128); background: none;"><span class="cite-accessibility-label" style="top: -99999px; clip: rect(1px 1px 1px 1px); overflow: hidden; position: absolute !important; padding: 0px !important; border: 0px !important; height: 1px !important; width: 1px !important; -webkit-user-select: none;">Jump up^</a> Catanho, M.; Mascarenhas, D.; Degrave, W.; De Miranda, A. B. ?L. (2006). "BioParser".Applied Bioinformatics 5 (1): 49–53. <a href="http://en.wikipedia.org/wiki/Digital_object_identifier" title="Digital object identifier" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">doi</a>:<a rel="nofollow" class="external text" href="http://dx.doi.org/10.2165%2F00822942-200605010-00007" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">10.2165/00822942-200605010-00007</a>.<a href="http://en.wikipedia.org/wiki/PubMed_Identifier" title="PubMed Identifier" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">PMID</a> <a rel="nofollow" class="external text" href="http://www.ncbi.nlm.nih.gov/pubmed/16539538" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">16539538</a>. <a class="external text" href="http://en.wikipedia.org/w/index.php?title=Template:Cite_doi/10.2165.2F00822942-200605010-00007&action=edit&editintro=Template:Cite_doi/editintro2" style="text-decoration: none; color: rgb(102, 51, 102); padding: 0px !important; background: none !important;">edit</a></li>
<li id="cite_note-10" style="margin-bottom: 0.1em; -webkit-column-break-inside: avoid; page-break-inside: avoid;"><a href="http://en.wikipedia.org/wiki/BioPerl#cite_ref-10" style="text-decoration: none; color: rgb(11, 0, 128); background: none;"><span class="cite-accessibility-label" style="top: -99999px; clip: rect(1px 1px 1px 1px); overflow: hidden; position: absolute !important; padding: 0px !important; border: 0px !important; height: 1px !important; width: 1px !important; -webkit-user-select: none;">Jump up^</a> Wei, X.; Kuhn, D. N.; Narasimhan, G. (2003). "Degenerate primer design via clustering".Proceedings / IEEE Computer Society Bioinformatics Conference. IEEE Computer Society Bioinformatics Conference 2: 75–83. <a href="http://en.wikipedia.org/wiki/PubMed_Identifier" title="PubMed Identifier" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">PMID</a> <a rel="nofollow" class="external text" href="http://www.ncbi.nlm.nih.gov/pubmed/16452781" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">16452781</a>. <a class="external text" href="http://en.wikipedia.org/w/index.php?title=Template:Cite_pmid/16452781&action=edit&editintro=Template:Cite_pmid/editintro2" style="text-decoration: none; color: rgb(102, 51, 102); padding: 0px !important; background: none !important;">edit</a></li>
<li id="cite_note-11" style="margin-bottom: 0.1em; -webkit-column-break-inside: avoid; page-break-inside: avoid;"><a href="http://en.wikipedia.org/wiki/BioPerl#cite_ref-11" style="text-decoration: none; color: rgb(11, 0, 128); background: none;"><span class="cite-accessibility-label" style="top: -99999px; clip: rect(1px 1px 1px 1px); overflow: hidden; position: absolute !important; padding: 0px !important; border: 0px !important; height: 1px !important; width: 1px !important; -webkit-user-select: none;">Jump up^</a> Croce, O.; Lamarre, M. L.; Christen, R. (2006). <a rel="nofollow" class="external text" href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1403806" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">"Querying the public databases for sequences using complex keywords contained in the feature lines"</a>. BMC Bioinformatics 7: 45. <a href="http://en.wikipedia.org/wiki/Digital_object_identifier" title="Digital object identifier" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">doi</a>:<a rel="nofollow" class="external text" href="http://dx.doi.org/10.1186%2F1471-2105-7-45" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">10.1186/1471-2105-7-45</a>. <a href="http://en.wikipedia.org/wiki/PubMed_Central" title="PubMed Central" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">PMC</a> <a rel="nofollow" class="external text" href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1403806" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">1403806</a>. <a href="http://en.wikipedia.org/wiki/PubMed_Identifier" title="PubMed Identifier" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">PMID</a> <a rel="nofollow" class="external text" href="http://www.ncbi.nlm.nih.gov/pubmed/16441875" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">16441875</a>.<a class="external text" href="http://en.wikipedia.org/w/index.php?title=Template:Cite_doi/10.1186.2F1471-2105-7-45&action=edit&editintro=Template:Cite_doi/editintro2" style="text-decoration: none; color: rgb(102, 51, 102); padding: 0px !important; background: none !important;">edit</a></li>
<li id="cite_note-12" style="margin-bottom: 0.1em; -webkit-column-break-inside: avoid; page-break-inside: avoid;"><a href="http://en.wikipedia.org/wiki/BioPerl#cite_ref-12" style="text-decoration: none; color: rgb(11, 0, 128); background: none;"><span class="cite-accessibility-label" style="top: -99999px; clip: rect(1px 1px 1px 1px); overflow: hidden; position: absolute !important; padding: 0px !important; border: 0px !important; height: 1px !important; width: 1px !important; -webkit-user-select: none;">Jump up^</a> Landsteiner, B. R.; Olson, M. R.; Rutherford, R. (2005). <a rel="nofollow" class="external text" href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160193" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">"Current Comparative Table (CCT) automates customized searches of dynamic biological databases"</a>. Nucleic Acids Research 33 (Web Server issue): W770–W773. <a href="http://en.wikipedia.org/wiki/Digital_object_identifier" title="Digital object identifier" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">doi</a>:<a rel="nofollow" class="external text" href="http://dx.doi.org/10.1093%2Fnar%2Fgki432" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">10.1093/nar/gki432</a>.<a href="http://en.wikipedia.org/wiki/PubMed_Central" title="PubMed Central" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">PMC</a> <a rel="nofollow" class="external text" href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160193" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">1160193</a>. <a href="http://en.wikipedia.org/wiki/PubMed_Identifier" title="PubMed Identifier" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">PMID</a> <a rel="nofollow" class="external text" href="http://www.ncbi.nlm.nih.gov/pubmed/15980582" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">15980582</a>. <a class="external text" href="http://en.wikipedia.org/w/index.php?title=Template:Cite_doi/10.1093.2Fnar.2Fgki432&action=edit&editintro=Template:Cite_doi/editintro2" style="text-decoration: none; color: rgb(102, 51, 102); padding: 0px !important; background: none !important;">edit</a></li>
<li id="cite_note-13" style="margin-bottom: 0.1em; -webkit-column-break-inside: avoid; page-break-inside: avoid;"><a href="http://en.wikipedia.org/wiki/BioPerl#cite_ref-13" style="text-decoration: none; color: rgb(11, 0, 128); background: none;"><span class="cite-accessibility-label" style="top: -99999px; clip: rect(1px 1px 1px 1px); overflow: hidden; position: absolute !important; padding: 0px !important; border: 0px !important; height: 1px !important; width: 1px !important; -webkit-user-select: none;">Jump up^</a> Llabrés, M.; Rocha, J.; Rosselló, F.; Valiente, G. (2006). "On the Ancestral Compatibility of Two Phylogenetic Trees with Nested Taxa". Journal of Mathematical Biology 53 (3): 340–364. <a href="http://en.wikipedia.org/wiki/Digital_object_identifier" title="Digital object identifier" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">doi</a>:<a rel="nofollow" class="external text" href="http://dx.doi.org/10.1007%2Fs00285-006-0011-4" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">10.1007/s00285-006-0011-4</a>. <a href="http://en.wikipedia.org/wiki/PubMed_Identifier" title="PubMed Identifier" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">PMID</a> <a rel="nofollow" class="external text" href="http://www.ncbi.nlm.nih.gov/pubmed/16823581" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">16823581</a>. <a class="external text" href="http://en.wikipedia.org/w/index.php?title=Template:Cite_doi/10.1007.2Fs00285-006-0011-4&action=edit&editintro=Template:Cite_doi/editintro2" style="text-decoration: none; color: rgb(102, 51, 102); padding: 0px !important; background: none !important;">edit</a></li>
<li id="cite_note-14" style="margin-bottom: 0.1em; -webkit-column-break-inside: avoid; page-break-inside: avoid;"><a href="http://en.wikipedia.org/wiki/BioPerl#cite_ref-14" style="text-decoration: none; color: rgb(11, 0, 128); background: none;"><span class="cite-accessibility-label" style="top: -99999px; clip: rect(1px 1px 1px 1px); overflow: hidden; position: absolute !important; padding: 0px !important; border: 0px !important; height: 1px !important; width: 1px !important; -webkit-user-select: none;">Jump up^</a> Pampanwar, V.; Engler, F.; Hatfield, J.; Blundy, S.; Gupta, G.; Soderlund, C. (2005). <a rel="nofollow" class="external text" href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1104167" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">"FPC Web Tools for Rice, Maize, and Distribution"</a>. Plant Physiology 138 (1): 116–126.<a href="http://en.wikipedia.org/wiki/Digital_object_identifier" title="Digital object identifier" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">doi</a>:<a rel="nofollow" class="external text" href="http://dx.doi.org/10.1104%2Fpp.104.056291" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">10.1104/pp.104.056291</a>. <a href="http://en.wikipedia.org/wiki/PubMed_Central" title="PubMed Central" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">PMC</a> <a rel="nofollow" class="external text" href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1104167" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">1104167</a>. <a href="http://en.wikipedia.org/wiki/PubMed_Identifier" title="PubMed Identifier" class="mw-redirect" style="text-decoration: none; color: rgb(11, 0, 128); background: none;">PMID</a> <a rel="nofollow" class="external text" href="http://www.ncbi.nlm.nih.gov/pubmed/15888684" style="text-decoration: none; color: rgb(102, 51, 102); padding-right: 13px; background: linear-gradient(transparent, transparent) 100% 50% no-repeat, url(data:image/svg+xml,%3C%3Fxml%20version%3D%221.0%22%20encoding%3D%22UTF-8%22%3F%3E%3Csvg%20xmlns%3D%22http%3A%2F%2Fwww.w3.org%2F2000%2Fsvg%22%20width%3D%2210%22%20height%3D%2210%22%3E%3Cg%20transform%3D%22translate%28-826.429%20-698.791%29%22%3E%3Crect%20width%3D%225.982%22%20height%3D%225.982%22%20x%3D%22826.929%22%20y%3D%22702.309%22%20fill%3D%22%23fff%22%20stroke%3D%22%2306c%22%2F%3E%3Cg%3E%3Cpath%20d%3D%22M831.194%20698.791h5.234v5.391l-1.571%201.545-1.31-1.31-2.725%202.725-2.689-2.689%202.808-2.808-1.311-1.311z%22%20fill%3D%22%2306f%22%2F%3E%3Cpath%20d%3D%22M835.424%20699.795l.022%204.885-1.817-1.817-2.881%202.881-1.228-1.228%202.881-2.881-1.851-1.851z%22%20fill%3D%22%23fff%22%2F%3E%3C%2Fg%3E%3C%2Fg%3E%3C%2Fsvg%3E) 100% 50%;">15888684</a>. <a class="external text" href="http://en.wikipedia.org/w/index.php?title=Template:Cite_doi/10.1104.2Fpp.104.056291&action=edit&editintro=Template:Cite_doi/editintro2" style="text-decoration: none; color: rgb(102, 51, 102); padding: 0px !important; background: none !important;">edit</a></li>
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