Difference between revisions of "KSH 0608 Bioinformatics with Bioperl"

Revision as of 19:45, 14 June 2016

From today, I will learn and summarize how to use Bioperl by reading a book "Bioinformatics with bioperl (Author: Young-Chang Kim)"

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 <p>From today, I will learn and summarize how to use Bioperl&nbsp;by reading a book &quot;Bioinformatics with bioperl (Author: Young-Chang Kim)&quot;</p>
-<p>1. Change DNA sequence to RNA sequence</p>
+<p>[[How to install Perl and BioPerl]]</p>
-<p>$DNASeq = &#39;GATACAA.......&#39;</p>
+<p>[[Transcription from DNA sequence to RNA sequence]]</p>
-<p>$RNASeq =~s/T/U/g;</p>
+<p>[[DATA extraction from FASTA]]</p>
-<p>=~ : binding operator tells Perl to match the pattern on the right against the string on the left</p>
+<p>[[Motif search]]</p>
-<p>(http://docstore.mik.ua/orelly/perl4/lperl/ch09_03.htm)</p>
+<p>[[Getting DNA information from NCBI]]</p>
-<p>s/ / / : substitution function, s is substitution operator, / is used to make a distinction</p>
-<p>g : pattern modifier from start to end</p>
 <p>&nbsp;</p>
-<p>==&gt; We can utilize the =~s/ / /g to the first homework</p>
-<p>If there is a certain DNA sequence, we can change the sequence into matching amino acid sequence</p>
-<p>For example, Methionine has AUG codon sequence and its template DNA sequence is 3&#39;-TAC-5&#39;.</p>
-<p>Thus, if we change the CAT sequence into M or Met, we could find the methionine from DNA sequence.</p>
-<p>&nbsp;Ex) $Methionine = ~s/CAT/M/g;</p>
-<p>Likewise, we could derive whole amino acids from DNA sequence.</p>
 <p>&nbsp;</p>
 <p>&nbsp;</p>