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KSH 0608 Bioinformatics with Bioperl

720 bytes removed, 19:45, 14 June 2016
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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 [[How to RNA sequenceinstall Perl and BioPerl]]</p>
<p>$DNASeq = &#39;GATACAA.......&#39;[[Transcription from DNA sequence to RNA sequence]]</p>
<p>$RNASeq =~s/T/U/g;[[DATA extraction from FASTA]]</p>
<p>=~ : binding operator tells Perl to match the pattern on the right against the string on the left[[Motif search]]</p>
<p>(http://docstore.mik.ua/orelly/perl4/lperl/ch09_03.htm)</p> <p>s/ / / : substitution function, s is substitution operator, / is used to make a distinction</p> <p>g : pattern modifier [[Getting DNA information from start to endNCBI]]</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>
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