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<h1p>BioinformaticsBack to [[Baik BuKyung]]</h1p> <hr /><p><span style="font-size:24px">Source code:</span></p> <hr /><div><div>#!/usr/bin/perl<br /> use strict;<br /> use warnings;<br /> open FH, ">", "outer.fasta" or die "$!\n";<br /> my $numberofseq=0;<br /> my @matrix;<br /> while(<>){<br /> if($_=~ />/){<br /> $matrix[$numberofseq]{seqname}=$_;<br /> $matrix[$numberofseq]{seqname}=~ s/\n//;<br /> <br />}<br /> else{<br /> $matrix[$numberofseq]{seq}=$_;<br /> $matrix[$numberofseq]{seq}=~ s/\n//;<br /> $numberofseq++;<br />}<br />}</div> <div> </div> <div>for(my $i=0;$i<$numberofseq;$i++){<br /> my $count=0;<br /> $matrix[$i]{seqlen}=length($matrix[$i]{seq});<br /> for(my $j=0;$j<$matrix[$i]{seqlen};$j++){<br /> my $seq_char=substr($matrix[$i]{seq},$j,1);<br /> if($seq_char=~/[GC]/){<br /> $count++;<br /> }<br /> $matrix[$i]{GC}=$count;<br /> }<br />}</div> <div> </div> <div>my $total_seqlen=0;<br />my $total_GC=0;<br />for(my $i=0;$i<$numberofseq;$i++){<br /> print FH ($matrix[$i]{seqname},"\n",$matrix[$i]{seq},"\n GC content is:",$matrix[$i]{GC},"\n");<br /> $total_seqlen=$total_seqlen+$matrix[$i]{seqlen};<br /> $total_GC=$total_GC+$matrix[$i]{GC};<br />}<br />print FH ("Average sequence length is :",$total_seqlen/$numberofseq,"\n GC contents:",$total_GC/$total_seqlen,"\n AT contents:",1-($total_GC/$total_seqlen),"\n")</div></div> <div><hr /><p> </p> <p><img alt="" src="/ckfinder/userfiles/images/%EC%BA%A1%EC%B2%9818.PNG" style="height:631px; width:1162px" /></p> <p> </p></div> <div><hr /><p> </p> <p><span style="font-size:24px">Result</span></p> <p><img alt="" src="/ckfinder/userfiles/images/%EC%BA%A1%EC%B2%9819.PNG" style="height:20px; width:406px" /></p> <p> </p> <p><span style="font-size:16px">After the 6.pl is executed with the 5_100-length_Seq.fasta file, the outer.fasta file is generated.</span></p> <p><span style="font-size:16px">The original content in the tert_Human.fasta file contains 5 fasta sequences with each length 100. The made this file.</span></p> <p> </p> <p><em>>0<br />ACCACTACTAAGCGCATGAACGACTGTTAGGTTTCCGATGGCTGCTTGCGTTCCGTGTTCCAGCTGACTGGGCTGAACTATTTGTAATGTTGGTTGCACT<br />>1<br />CAGGTACACGGACTGTTTGGTTTGCCCAATTAATTGGCGGGTCGTAAACCGGTTTTTCGTTGGGCGCGGAGTTGTCGTAAACGGTCGGTATTAACTACCT<br />>2<br />ATATTCTGTTCGAAGGCGAGGCCTTAATAAACGGGCTCACACTATACGTTTCTAGCGTGCCAGTACGCGTATGCCCTGAGCAGCATCTTGAATAGTCCTT<br />>3<br />CACGTCTTGAGGCATGCTCACATAACTTGGGATTGATACAATCGGGGGACGGTAGCGGGGCTAGTGGGCATCGTCGGCGGTCTACGAGCAAAAGTATCAG<br />>4<br />CAGGACGTGAACCGAAAGCTGCACACCTATACTATCGTAGTATACCACCGTTCCGTAAATCCATCGCTGATCCTGCCATGAAGGGCTAAGTACGCATGAG</em><br /> </p> <p> </p> <p> </p> <p><span style="font-size:16px">The content of outer.fasta file is</span></p> <p> </p> <div><div><em>>0<br />ACCACTACTAAGCGCATGAACGACTGTTAGGTTTCCGATGGCTGCTTGCGTTCCGTGTTCCAGCTGACTGGGCTGAACTATTTGTAATGTTGGTTGCACT<br /> GC content is:0.49<br />>1<br />CAGGTACACGGACTGTTTGGTTTGCCCAATTAATTGGCGGGTCGTAAACCGGTTTTTCGTTGGGCGCGGAGTTGTCGTAAACGGTCGGTATTAACTACCT<br /> GC content is:0.5<br />>2<br />ATATTCTGTTCGAAGGCGAGGCCTTAATAAACGGGCTCACACTATACGTTTCTAGCGTGCCAGTACGCGTATGCCCTGAGCAGCATCTTGAATAGTCCTT<br /> GC content is:0.48<br />>3<br />CACGTCTTGAGGCATGCTCACATAACTTGGGATTGATACAATCGGGGGACGGTAGCGGGGCTAGTGGGCATCGTCGGCGGTCTACGAGCAAAAGTATCAG<br /> GC content is:0.55<br />>4<br />CAGGACGTGAACCGAAAGCTGCACACCTATACTATCGTAGTATACCACCGTTCCGTAAATCCATCGCTGATCCTGCCATGAAGGGCTAAGTACGCATGAG<br /> GC content is:0.5</em></div> <div> </div> <div><br /><em>Average sequence length is :100<br /> GC contents:0.504<br /> AT contents:0.496</em></div></div> <div> </div> <div> </div> <div><span style="font-size:16px">I just add GC content of each sequence to the end of each sequence. At the end of the file, Average sequence length, GC contents and AT contents are printed.</span></div></div>
