Difference between revisions of "DATA extraction from FASTA"

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imported>Seung-hoon Kim
(Created page with "<p>FASTA format is an arranged sequence data file.</p> <p>FASTA file starts from > in the first row.</p> <p>This row contains basic information such as sequence ID.</p> <p>...")
 
imported>Seung-hoon Kim
 
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<p>&nbsp;</p>
 
<p>&nbsp;</p>
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<p>4. Using &lt;STDIN&gt;, we can open the file in a perl program</p>
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<p>Ex) print &quot;Please type the filename to extract: &quot;;</p>
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<p>$DNAfilename = &lt;STDIN&gt;;</p>
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<p>chomp $DNAfilename;</p>
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<p>open(DNAFILE, $DNAfilename);</p>
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<p>@FileData = &lt;DNAFILE&gt;;</p>
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<p>close DNAFILE;</p>
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<p>print @FileData;</p>
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<p>exit;</p>
  
 
<h3><span style="background-color:rgb(245,245,255); color:rgb(0,0,0)">Reference</span></h3>
 
<h3><span style="background-color:rgb(245,245,255); color:rgb(0,0,0)">Reference</span></h3>
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<p>[[<a href="http://biolecture.org/index.php/KSH_0608_Bioinformatics_with_Bioperl" title="KSH 0608 Bioinformatics with Bioperl">KSH_0608 Bioinformatics with Bioperl</a>]]</p>
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<p><a href="http://biolecture.org/index.php/KSH_0608_Bioinformatics_with_Bioperl" title="KSH 0608 Bioinformatics with Bioperl">KSH_0608 Bioinformatics with Bioperl</a></p>

Latest revision as of 21:38, 14 June 2016

FASTA format is an arranged sequence data file.

FASTA file starts from > in the first row.

This row contains basic information such as sequence ID.

1. Go to the NCBI (http://www.ncbi.nlm.nih.gov/) , National Center for Biotechnology Information

2. Choose the database that you want and search the information that you want to find

Ex) Database - Gene / Search - Homo sapiens chromosome 2 / Choose what you want to look at

3. Choose FASTA from the 'Go to nucleotide' section

1)Display settings: FASTA

Send to: File

You get a link like this:

http://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?tool=portal&sendto=on&log$=seqview&db=nuccore&dopt=fasta&val=51466650&extrafeat=0&maxplex=1

 

4. Using <STDIN>, we can open the file in a perl program

Ex) print "Please type the filename to extract: ";

$DNAfilename = <STDIN>;

chomp $DNAfilename;

open(DNAFILE, $DNAfilename);

@FileData = <DNAFILE>;

close DNAFILE;

print @FileData;

exit;

Reference

1) http://seqanswers.com/forums/showthread.php?t=18354

 

KSH_0608 Bioinformatics with Bioperl

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