Changes

<p>Back to [[Baik BuKyung]]</p> <hr /><p><span style="font-size:24px">Source code:</span></p> <hr /><div><div>#!/usr/bin/perl<br />&nbsp;use strict;<br />&nbsp;use warnings;<br />&nbsp;open FH, &quot;&gt;&quot;, &quot;outer.fasta&quot; or die &quot;$!\n&quot;;<br />&nbsp;my $numberofseq=0;<br />&nbsp;my @matrix;<br />&nbsp;while(&lt;p&gt;This is Sungwon's Bioinformatics Lecture Note){<br />&ltnbsp;if($_=~ /p&gt;/){<br />&ltnbsp;p&gtnbsp;$matrix[$numberofseq]{seqname}=$_;<br />&nbsp;&nbsp;$matrix[Biopedia by SungwonJeon$numberofseq]{seqname}=~ s/\n//;<br />&nbsp;&nbsp;<br />}<br />&nbsp;else{<br />&nbsp;&nbsp;$matrix[$numberofseq]{seq}=$_;<br />&nbsp;&ltnbsp; &nbsp;$matrix[$numberofseq]{seq}=~ s/\n//;<br /p>&nbsp;&gtnbsp;$numberofseq++;<br />}<br />}</div> <div>&nbsp;</div> <div>for(my $i=0;$i&lt;h1$numberofseq;$i++){<br />&nbsp;my $count=0;<br />&gtnbsp;$matrix[$i]{seqlen}=length($matrix[$i]{seq});<br />&nbsp;for(my $j=0;Principles of Bioinformatics$j&lt;$matrix[$i]{seqlen};$j++){<br /h1>&gtnbsp;&nbsp;my $seq_char=substr($matrix[$i]{seq},$j,1);<br />&ltnbsp;p&gtnbsp;if($seq_char=~/[GC]/){<br />&ampnbsp;&nbsp;&ltnbsp;$count++;<br /p>&nbsp;&gtnbsp;}<br />&ltnbsp;h1&gtnbsp;$matrix[$i]{GC}=$count;Bioprogramming<br />&ltnbsp;}<br />}</h1div> <div>&gtnbsp;</div> <div>my $total_seqlen=0;<br />my $total_GC=0;<br />for(my $i=0;$i&lt;p$numberofseq;$i++){<br />&nbsp;print FH ($matrix[$i]{seqname},&quot;\n&quot;,$matrix[$i]{seq},&gtquot;Human DNA has about 3 billion base pairs in a single cell. It \n GC content is 2.79 GB text :&quot;,$matrix[$i]{GC},&quot;\n&quot;);<br />&nbsp;$total_seqlen=$total_seqlen+$matrix[$i]{seqlen};<br />&nbsp;$total_GC=$total_GC+$matrix[$i]{GC};<br />}<br />print FH (1 letter &quot;Average sequence length is 1 byte). However:&quot;,$total_seqlen/$numberofseq,&quot;\n GC contents:&quot;,$total_GC/$total_seqlen, when Human DNA is sequenced&quot;\n AT contents:&quot;, it may be sequenced 30X or more DNA 1-(In case of NGS(Next Generation Sequencing$total_GC/$total_seqlen),&quot;\n&quot;)</div></div> <div><hr /><p>&nbsp;</p> <p><img alt="" src="/ckfinder/userfiles/images/%EC%BA%A1%EC%B2%9818. So Raw sequenced DNA text file PNG" style="height:631px; width:1162px" /></p> <p>&nbsp;</p></div> <div><hr /><p>&nbsp;</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>&nbsp;</p> <p><span style="font-size:16px">After the 6.pl is more than 84 GBexecuted with the 5_100-length_Seq. Because of large amount of Raw datafasta file, it the outer.fasta file is difficult to analyze Raw data with our handsgenerated. That's why we need computer </span></ computer program to analyze NGS datap> <p><span style="font-size:16px">The original content in the tert_Human. We are not enough smart to analyze NGS datafasta file contains 5 fasta sequences with each&nbsp;length 100. To deal with computer program, we should know what program is , what programming is, what computer isThe made this file.</span></p> <p>&ltnbsp;</p> <p><em>&gt;0<br />ACCACTACTAAGCGCATGAACGACTGTTAGGTTTCCGATGGCTGCTTGCGTTCCGTGTTCCAGCTGACTGGGCTGAACTATTTGTAATGTTGGTTGCACT<br />&ltgt;h21<br />CAGGTACACGGACTGTTTGGTTTGCCCAATTAATTGGCGGGTCGTAAACCGGTTTTTCGTTGGGCGCGGAGTTGTCGTAAACGGTCGGTATTAACTACCT<br />&gt;What is programming?2<br />ATATTCTGTTCGAAGGCGAGGCCTTAATAAACGGGCTCACACTATACGTTTCTAGCGTGCCAGTACGCGTATGCCCTGAGCAGCATCTTGAATAGTCCTT<br />&ltgt;3<br />CACGTCTTGAGGCATGCTCACATAACTTGGGATTGATACAATCGGGGGACGGTAGCGGGGCTAGTGGGCATCGTCGGCGGTCTACGAGCAAAAGTATCAG<br /h2>&gt;4<br />CAGGACGTGAACCGAAAGCTGCACACCTATACTATCGTAGTATACCACCGTTCCGTAAATCCATCGCTGATCCTGCCATGAAGGGCTAAGTACGCATGAG</em><br />