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POPerl: Search a pattern across array elements
 

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  1. POPerl: Search a pattern across array elements
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    <p>I am a Perl newbie, stuck with another bioinformatics problem that requires some help and input.</p> <p><strong>The problem in brief:</strong></p> <ol> <li><p>I have a file, which has over 40,000 <em>unique</em> DNA sequences. By unique, I mean unique sequence id. I am attaching a portion of it at the end of my post to help you show what it looks like.</p></li> <li><p>I need to divide <em>each</em> of the 40,000 sequences into 3 parts. So if a particular sequence is 999 character long, each of the 3 parts would have 333 characters. </p></li> <li><p>I need to look for the following pattern through each of the 3 individual parts: </p> <p>$gpat = [G]{3,5}; $npat = [A-Z]{1,25};<br> $pattern = $gpat.$npat.$gpat.$npat.$gpat.$npat.$gpat; </p></li> <li><p>If $pattern appears in the first of the 3 parts, increase the counter of 'beginning', if $pattern occurs in the 2nd of the 3 parts, increase counter of 'middle' and lastly if the $pattern appears in the 3rd part, increase counter of 'end'.</p></li> <li><p>Print the counters of 'beginning','middle' and 'end' i.e basically summation of 'beginning','middle','end' for each of the sequences. </p> <p>Say in 1st sequence, the values are like '2','5','3' respectively and in 2nd sequence, the values are '4','1','6', the final count should be '7,6,9'.</p></li> </ol> <p><strong>The issues I am having:</strong></p> <ol> <li>If a particular sequence is split into 3 parts, potential $pattern is lost. eg say on a sequence like :</li> </ol> <p>gggatgtcgatgcatggggatgcatcgatgcggggactagctagcgggatgctacgatggggatgatgataatatcgcggcgcatatatgctagtctatatatta</p> <p>a split into 3 parts produces following 3 sub-parts,each of 35 character length:</p> <p>gggatgtcgatgcatggggatgcatcgatgcgggg<br> actagctagcgggatgctacgatggggatgatgat<br> aatatcgcggcgcatatatgctagtctatatatta </p> <p>Hence, <em>$pattern gets split into the first 2 parts</em>. Is there anyway to say "If $pattern begins in 1st part and ends in 2nd part", increase count of "beginning" ? </p> <p><strong>##UPDATE##</strong> The following issue has been resolved thanks to the code suggested by Cupidvogel </p> <blockquote> <p>2.How do I divide a sequence into 3 parts if its length is not divisible by 3? I tried using <code>int</code>, but then the last part is 1-2 characters short.</p> </blockquote> <p>The following is the code I have written so far. </p> <p>It reads in the file, displays the header name and sequence, the length into which each sequence will be divided and finally the sequence split into 3 parts which works fine provided the sequence length is divisible by 3, for those which aren't, the final 3rd part is 1-2 characters short.</p> <pre><code>#Take Filename from user print "Please enter file name : "; $in =&lt;&gt;; chomp $in; open (FASTA,"$in") or die ; while (&lt;FASTA&gt;) { $/="&gt;"; @array = split '\n', $_; $header=shift @array; # Header of the fasta sequence print "\n\nNext sequence: \n"; print $header,"\n"; $seq= join '', @array; # sequence $seq=~s/\s//g; $seq=~s/\*//g; $seq=~s/&gt;//g; print $seq,"\n\n"; $num = int(length($seq)/3); @arr = unpack("A$num A$num A*",$seq); print " New method gives this :", @arr; print "\nThe first element is :", $arr[0]; print "\nThe second element is :",$arr[1]; print "\nThe third element is :",$arr[2] ; #The following lines of code were originally written to split... #...the sequence into 3 parts, albeit unsuccessfully #my $split = (length $seq)/3; #print $split,"\n\n"; #my $int = int $split; #print $int,"\n\n"; #my @array2 = $seq =~ /(.{$int})/g; #print join (" ", @array2),"\n\n"; #print $array2[0],"\n",$array2[1],"\n",$array2[2]; } exit; </code></pre> <p>I have been trying the code I have written so far with the following sample file : sample.fa</p> <pre><code>&gt;ABC_123 2 atgtcgatcgatcggcgggcatgcgcgcgcggatg atatatagcgcgcgctatatagcgcgactctacgc atgctgctgactagctatagtcgctgactgcgcgt gggaaaaagggcccgggccccgttttggggatcta ggggatagctgatgctagcatgcatgctgactgca &gt;DEF_456 4 gggatgtcgatgcatggggatgcatcgatgcgggg actagctagcgggatgctacgatggggatgatgat aatatcgcggcgcatatatgctagtctatatatta &gt;GHI_789 1 atagctgctagtcgatcggcgcgggtatcgatcgg ggatcgatcgatcggggatcgatcgggggatcgat </code></pre> <p>The actual input file looks like the following:</p> <pre><code>&gt;NR_037701 1 aggagctatgaatattaatgaaagtggtcctgatgcatgcatattaaaca tgcatcttacatatgacacatgttcaccttggggtggagacttaatattt aaatattgcaatcaggccctatacatcaaaaggtctattcaggacatgaa ggcactcaagtatgcaatctctgtaaacccgctagaaccagtcatggtcg gtgggctccttaccaggagaaaattaccgaaatcactcttgtccaatcaa agctgtagttatggctggtggagttcagttagtcagcatctggtggagct gcaagtgttttagtattgtttatttagaggccagtgcttatttagctgct agagaaaaggaaaacttgtggcagttagaacatagtttattcttttaagt gtagggctgcatgacttaacccttgtttggcatggccttaggtcctgttt gtaatttggtatcttgttgccacaaagagtgtgtttggtcagtcttatga cctctattttgacattaatgctggttggttgtgtctaaaccataaaaggg aggggagtataatgaggtgtgtctgacctcttgtcctgtcatggctggga actcagtttctaaggtttttctggggtcctctttgccaagagcgtttcta ttcagttggtggaggggacttaggattttatttttagtttgcagccaggg tcagtacatttcagtcacccccgcccagccctcctgatcctcctgtcatt cctcacatcctgtcattgtcagagattttacagatatagagctgaatcat ttcctgccatctcttttaacacacaggcctcccagatctttctaacccag gacctacttggaaaggcatgctgggtctcttccacagactttaagctctc cctacaccagaatttaggtgagtgctttgaggacatgaagctattcctcc caccaccagtagccttgggctggcccacgccaactgtggagctggagcgg gagggaggagtacagacatggaattttaattctgtaatccagggcttcag ttatgtacaacatccatgccatttgatgattccaccactccttttccatc tcccagaagcctgctttttaatgcccgcttaatattatcagagccgagcc tggaatcaaactgcctctttcaaaacctgccactatatcctggctttgtg acctcagccaagttgcttgactattctcagtctcagtttctgcacctgtc aaatagggtttatgttaacctaactttcagggctgtcaggattaaatgag catgaaccacataaaatgtttggtgtatagtaagtgtacagtaaatactt ccattatcagtccctgcaattctatttttcttccttctctacacagcccc tgtctggctttaaaatgtcctgccctgctttttatgagtggataccccca gccctatgtggattagcaagttaagtaatgacactcagagacagttccat ctttgtccataacttgctctgtgatccagtgtgcatcactcaaacagact atctcttttctcctacaaaacagacagctgcctctcagataatgttgggg gcataggaggaatgggaagcccgctaagagaacagaagtcaaaaacagtt gggttctagatgggaggaggtgtgcgtgcacatgtatgtttgtgtttcag gtcttggaatctcagcaggtcagtcacattgcagtgtgtcgcttcacctg gctccctcttttaaagattttccttccctctttccaactccctgggtcct ggatcctccaacagtgtcagggttagatgccttttatgggccacttgcat tagtgtcctgatagaggcttaatcactgctcagaaactgccttctgccca ctggcaaagggaggcaggggaaatacatgattctaattaatggtccaggc agagaggacactcagaatttcaggactgaagagtatacatgtgtgtgatg gtaaatgggcaaaaatcatcccttggcttctcatgcataatgcatgggca cacagactcaaaccctctctcacacacatacacatatacattgttattcc acacacaaggcataatcccagtgtccagtgcacatgcatacacgcacaca ttcccttcctaggccactgtattgctttcctagggcatcttcttataaga caccagtcgtataaggagcccaccccactcatctgagcttatcaaccaat tacattaggaaagactgtatttcctagtaaggtcacattcagtagtactg agggttgggacttcaacacagctttttgggggatcataattcaacccatg acagccactgagattattatatctccagagaataaatgtgtggagttaaa aggaagatacatgtggtacaaggggtggtaaggcaagggtaaaaggggag ggaggggattgaactagacacagacacatgagcaggactttggggagtgt gttttatatctgtcagatgcctagaacagcacctgaaatatgggactcaa tcattttagtccccttctttctataagtgtgtgtgtgcggatatgtgtgc tagatgttcttgctgtgttaggaggtgataaacatttgtccatgttatat aggtggaaagggtcagactactaaattgtgaagacatcatctgtctgcat ttattgagaatgtgaatatgaaacaagctgcaagtattctataaatgttc actgttattagatattgtatgtctttgtgtccttttattcatgaattctt gcacattatgaagaaagagtccatgtggtcagtgtcttacccggtgtagg gtaaatgcacctgatagcaataacttaagcacacctttataatgacccta tatggcagatgctcctgaatgtgtgtttcgagctagaaaatccgggagtg gccaatcggagattcgtttcttatctataatagacatctgagcccctggc ccatcccatgaaacccaggctgtagagaggattgaggccttaagttttgg gttaaatgacagttgccaggtgtcgctcattagggaaaggggttaagtga aaatgctgtataaactgcatgatgtttgcaggcagttgtggttttcctgc ccagcctgccaccaccgggccatgcggatatgttgtccagcccaacacca caggaccatttctgtatgtaagacaattctatccagcccgccacctctgg actccctcccctgtatgtaagccctcaataaaaccccacgtctcttttgc tggcaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa aaa &gt;NM_198399 1 aacagattttaactctgaaaagccatttccagtgtctatagactattgtg agcctggagaagtagcatttagttgggatagcttcactagagctgcctgc caaagacttccttccacaggatcttgtcgcaccagcaactgacaggagct tgggagctcgggagcttgggagagggcttatgtttttaataatgtagctg tcagttcgaagcctggaaatgttgaccctcaaagggcataaaatcttgtt attttaatttgcatctgggagaatgtctgagcaaggagacctgaatcagg caatagcagaggaaggagggactgagcaggagacggccactccagagaac ggcattgttaaatcagaaagtctggatgaagaggagaaactggaactgca gaggcggctggaggctcagaatcaagaaagaagaaaatccaagtcaggag caggaaaaggtaaactgactcgcagccttgctgtctgtgaggaatcttct gccagaccaggaggtgaaagtcttcaggatcagactctctgaaaactgca aatggaaaggaattcaaaagaatttagattaaaagttaaataaaaagtag gcacagtagtgctgaattttcctcaaaggctctcttttgataaggctgaa ccaaatataatcccaagtatcctctctccttccttgttggagatgtctta cctctcagctccccaaaatgcacttgcctataagaaacacaattgctggt tcatatgaaacttaggaaatagtgaataaggtgcatttaactttggagaa atacttttatggctttggtggagatttctcaatactgcaaaagttgtcca gaaatgaatctgagctgatggtgactttaagttaatattattaatatatc actgcatatttttacccttatttttgctccttacagcaagattagtaggt tataaaaatttaaatttaaacaaaattatttcatgacaaaatgggaaact tcacatcatacttatttttgtttgcctttcaggcatcatattagctttta taaaaaatggtcttgctgctgaaattgtacttattttatcagaggctggg tgcagtcaagacaaaagtaaaatggtttacctgagcccaggggagggaaa attgattaagatatcattatttttgtttggtttggttttgcttttttcct cttactttaattgaaatactctgaattcccctcatggaaacagagagcat tgagagcactttctttaaaaggaccaaaaataaattcctaatagattttg tcctaagagagtgtttttttttctagcatcattttctttacatgccactc atgtcataaggcatggacaggctatctttcagtggccattactatgtttc gtacacatgctttattttacttgggctctgagaaatgtgtggctttcctt cagcattttatttgtgcttctctttttaatggagattgaaaagggagaat aatgtgaatatcacggcttatattattaaatgttgattgatggcttgtaa tgtactgcacacaatatatgttaactctgcagaatgacagaccctgggag aagtaatgccccagttgtcccccactcctaatgccaggcagagaaggaca gcctttatagacttaatctgctttttgtcccatttgacaaggtaccagga ggaaattttttaagggatcaactgtatcacagtgcccactctggacctaa gtctagtgtatccatacaattggtgcagagaaataaggtgtaaatggtgc tttgttcctgctggttccaagctcagaaaccaagactagctttgtaggag agaatgagagcctgcaagcctctctttggattggctgaggagtggtggga gcagggggttgatagaaaacatccagacacacatataagcaagtggccgt gctacctttttagagaataaagaaacagacttttgagtttatatgcaatg ccttcattaggtaccaccggcacttacaaaatgtgcggactgaatcccag agaacactggcagatgtatacagtatatggattgtatcgcttccccaatg tttgtaaattcacagtatttggaaaactgccttcattttccagtgtggga aaaactcttgctacctgtattacttgatctcagacccatacctgatggtt cagtctgtccttaagttaaaagaattttgcttttctaatgttatactatt tacctgtcagtgtattactgcaacttgaatcactcttttactgttgttgg atataaacttatcctgtaccaatgtatttattaacacttgtattttatta ttgagcatatcaataaaaatattaaaaaataacagattgttttttaccaa aaaaaaaaaaaaa &gt;NR_026816 1 caacccactctctgtgctatgacttcattactctttcccagcccagccct gggcaagccccttacgaagtctcaggctacctggatgaccaccctttctt atgatgctgcaaggagggcaggtgggcagagccccgtgcatcctgggctc aggccagggacccaagagcttgggagaagctggttctcagactgaaggcc agagcccagcaccttgtcaccatcccggggagcatcatggcacacaacaa ccagagccaaggctacagctagagagttgactcctctatttgagattgac aggcctcggaagtcaaaataagtggtttcctagaccgggtcgagagcaag tctctattggtcccaactgagttttttcagctggtttttcaaccaaacag cacctcatctcccagtgaggggaagggaaggctgggctgagagcagcaag gctgctcatctcacctctccccacccagccatgccagccgcctcacctgg tggggagaggtgggcctcacctgggtcccctggcagtgctctgtgaaggg tcttgacattgcactgtaataataaaggtgtgtgtgaagtatcaaaaaaa &gt;NR_027917 1 atgaagatgattgagcagcacaatcaggaatacagggaagggaaacacag cttcacaatggccatgaacgcctttggagaaatgaccagtgaagaattca ggcaggtggtgaatggctttcaaaaccagaagcacaggaaggggaaagtg ctccaggaacctctgcttcatgacatccgcaaatctgtggattggagaga gaaaggctacgtgactcctgtgaaggatcagtgcagctggggctctgtaa ggacagatgttaggaaaactgagaaactagtttcactgagtgtgcagacc tggtggactgctctaggcttcaaggcaatgttggctgcatttttggagaa ccattattttgcttccagtatgttgccgacaatggaggcctggactctga ggaatccttttcatatgaagaaaagctctggagactggaaagtccaaggt cacagaggtgcatctggtgagagccttcttgctagtggggaatctcagca gagtcctgaggtggcacagtattctgggaagcatcaagtgcagtgtcatc ttatcgaggaggctctgcagatgctaagtggtggggatgaggatcacgat gaagacaaatggccccatgacatgaggaatcatctggctggagaggccca ggtgtag &gt;NR_002777 3 cttgtcctttcagaagatcagagacaagtgatatctgtgccaatttggcc ttttcagtgttataattatggtgtcttgggatcccaatatttctcctaat gtttccctgatgtgatactttgagagcccaggatgccagtacaataattg aaattcacaaatgtctggtatcttgtccctcgtgccccatatattatctg tggtttcggagagctcacttgtctcttatcttcagaaatgacagcacatg aaatgttgtttggagccactgtcacatcaactgtagaaaaattaacaggt cagctaagggatataatgtaactttatttgtgatatgagagaaatcttga taaagacttgagagaaaactgggaggaaccttgtttagaagttataagga ggggtaagttatgtgtgtcttggaaggagaatcataaatcttaaaacatg agcctaatagagaacataaaattctaaaagataaagataataataatgat aagccgcagggtggcttatgataatgtgacttctccttaccccagtagcg tcggacatctgtcagctctgaaatgataaaaatgcacaatattgaataca aacaaaggagtcagcactgaaattcattttctctccagattagggaaaga gtaggtatgccctatggtagggcagtaaattgctgaatgatgagatgaaa cagccacctagccatttcccattaaatataatcccatcagcagcagacaa tatctatcctcccctatcccctctatccatatttggaaactgcaccctct tccctatttagcaccctaacaccacttgaattccataaccctgttgttga tctagctctcctcacctctaaacacttctagcattcctttcagatcagga gctcgaaacactctcctttgattttttggaaaagtttctggcttcttcaa ggtcacgttctccgtcctaagaattaaaaaaaaaaaaaaaaacttccaaa cctttgaccttgtgtccgtggaacacccctgacttcctatcatttcaacc cattgaggcacttgaactctcttcttggggatcctgagaagggagagtgc aaactcttgaccctggaggcaaacaaaatgttctcatgtttgccttccca cttactttctgtgagaacgtgggaagatcttaacctctcagaagcacagt ttcttccttctaaaatgaaataattaacctctccctgtctacattcttaa actcataggacataaaaaaaaaaaaaa &gt;NR_033769 1 ggcctctggcgggcctccagccagttagaccatttgactaggacgtgtgc agctcagccagccacagaactggaatttttcaggagcagggggagcatgg agtttggactttgctgagcaactgaagtggagcgcagagcttgctcgctt aggagagggcagcatggatggcaaacaagggggcatggatgggagcaagc ccacggggccaagagactctcctgacaccaggcttctttcaaacccattg atgggtgattctgtgtctgattggtctcctatgcctgaagctgcaatcta cggacatcagctgtctctgaggaacctcatcagccacgggtggcttgtga acatcatcatggcagatcatgtttccccactccatgaagcctgtctcaga ggtcatccctctcgtgtaaagattttattaaagcatggagctcaggtgaa tggcgtgacaacagactggcacactccactgtttaatgtttgtatcagca gcagctgggattatgcttctgcagcatggagccagcgttcaacctgagag tgatctggcatcccccgtccatgaagctgctaggagaggccacgtggagt gtgtcgactctcttacagcttataggggcaaaaatgaccataacatcagc cacgtgggcacttcactgtatttggcttgtgaaaaccagcagatagcctg tgtcaagaagcttctggagtcaggagcagacctgaacccagggagaggtt ccccacttcatgcagtggccttcatgaaggccctcatgaaggattcccca cttcatgcagtggccaggacagccagtgaagagctggcctgcctgctcat ggattttggagcagacacccaggccaagaatgctgaaggcaaatgtcatg tggagctggtgcctccagagagccctttgatccagctcttcttggagaga gaagggcccccttcttttgatgcagttatgcctagaaatcagaagggctt tggaatccagcagcatcataagataaccaaagtcgtcctcccagaggatc tgaaatggtttctcctacatctttgtatgtatcaatggaatggattcaca aacaatgtgaaaacattattgagtgttgtagccactagaattttaaaatc aagttaggtttatagagtttgactagttttttcgattagatttgtattag ttataaatttgttcatagagtttgactaattttttcgattagatttgtat ttgttaaactctgaagccagagtttaaacacactgcatacgtttgtatga ttagttagaaggcatgaagacttttttccctgcttggagactgtctaaaa taacagctattgttttgcatatccactgcaggccaagcactttcagcatc atctaattcagccctcacagcaactgggtcaatctgtccaatttcccagg gcaaggatagaggagtcagattcaaatacaggttttctgacgttaactta tgtgatgatttgatcaaagcaggattttccagcatcactatccttgttcc atctctgctatatgggaatgaaaataaagaaatgtatttcaaaaaaataa aaagaaaagaaaaacagagacggtc &gt;NM_016326 3 atgcgcgcaagagagcgggaagccgagctgggcgagaagtaggggagggc ggtgctccgccgcggtggcggttgctatcgcttcgcagaacctactcagg cagccagctgagaagagttgagggaaagtgctgctgctgggtctgcagac gcgatggataacgtgcagccgaaaataaaacatcgccccttctgcttcag tgtgaaaggccacgtgaagatgctgcggctggtgtttgcacttgtgacag cagtatgctgtcttgccgacggggcccttatttaccggaagcttctgttc aatcccagcggtccttaccagaaaaagcctgtgcatgaaaaaaaagaagt tttgtaattttatattactttttagtttgatactaagtattaaacatatt tctgtattcttccacatattttctgcagttattttaactcagtataggag ctagaggaagagatttccgaagtctgcaccccgcgcagagcactactgta acttccaagggagcgctgggagcagcgggatcgggttttccggcacccgg gcctgggtggcagggaagaatgtgccgggatccgcctcagggatctttga atctctttactgcctggctggccggcagctccg &gt;NM_181641 2 atgcgcgcaagagagcgggaagccgagctgggcgagaagtaggggagggc ggtgctccgccgcggtggcggttgctatcgcttcgcagaacctactcagg cagccagctgagaagagttgagggaaagtgctgctgctgggtctgcagac gcgatggataacgtgcagccgaaaataaaacatcgccccttctgcttcag tgtgaaaggccacgtgaagatgctgcggctggcactaactgtgacatcta tgaccttttttatcatcgcacaagcccctgaaccatatattgttatcact ggatttgaagtcaccgttatcttatttttcatacttttatatgtactcag acttgatcgattaatgaagtggttattttggcctttgcttgtgtttgcac ttgtgacagcagtatgctgtcttgccgacggggcccttatttaccggaag cttctgttcaatcccagcggtccttaccagaaaaagcctgtgcatgaaaa aaaagaagttttgtaattttatattactttttagtttgatactaagtatt aaacatatttctgtattcttccacatattttctgcagttattttaactca gtataggagctagaggaagagatttccgaagtctgcaccccgcgcagagc actactgtaacttccaagggagcgctgggagcagcgggatcgggttttcc ggcacccgggcctgggtggcagggaagaatgtgccgggatccgcctcagg gatctttgaatctctttactgcctggctggccggcagctccg &gt;NM_001144931 1 gtttccgttcctctgcccgccatgccgttcctagagctgcacacgaattt ccccgccaaccgagtgcccgcggggctggagaaacggctgtgcgccgtcg ctgcctccatcttgggcaaacctgcagaccttgtgaacgtgacggtacgg ccgggcctggccagggcgctgagcgggtccaccgagccctgcgcgcagct gtccatctcctccatcggcgtagtgggcaccgccgaggacaaccgcagcc acagtgcccacttctttgagtttctcaccaaggagctagccctgggccag gaccggtgcgcaggggtagtaggcccggaatattattctaaaacacaatc agagtactccattcctgctaacagtttaaagccaaacacctaggcaggcc atttaggcttctgaatgactgggtcttgaccaggagagctgctgtctagg ttttctcttcctgaccagttcctcaagagaaatgcaaaactagtgattaa cagtaagagtcaggcagggcgcggtggctcacgcctgtaatcccagcact ttgggaggccgag &gt;NR_029429 1 ggacaccaccccaaaatttcctagtcctctttgatacgggttcctccaat ctgtagctgccctccatctactgccagagccaagtctgctccaatcacaa caggttcaatcccagcctgtcctccaccttcagaaacgatggacaaacct atggactatcctatgggagtggcagcctgagtgtgttcctgggctatgac actgtgactgttcataacatcgttgtcaataaccaggagtttggcctgag tgagaatgagcccagcgaccccttttactattcagactttgacgggatcc tgggaatggcctacccaaacatggcagaggggaattcccctacagtaatg caggggatgctgcagcagagccagcttactcagcccgtcttcagcttcta cttcacctgccagccaacccgccagtattgtggagagctcatccttggag gtgtggaccccaactttattctggtcagatcatctggacccctgtcagcc cgtaactgtactggcagattgccatcgaggaatttgccatcggtaaccag gccactggcttgtgctctgagggttgccaggccattgtggataccgagac cttcctgc &gt;NR_026551 1 tgtggcctgagaggacggccaggactggccagaaaagagagggacgtggc taaacgtgagggggcgtggccaagatggccgcgtgcgggatcctcgggta ccgggagcgaacgaggaggttctggctcagtgcatccactctgggagagc gtggacctggttcctgggggcgatcgccagtcacccatcaacattcggtg gagggacagtgtttatgatcccggcttaaaaccactgaccatctcttatg acccagccacctgcctccacgtctggaataatgggtactctttcctcgtg gaatttgaagattctacagataaatcagctgcacttagtgcattggaacg cagtcaaatttgaaaactttgaggatgcagcactggaagaaaatggtttg gctgtgataggagtatttttaaagatttcggaaacttctggcagcccagt gtctactggaaggcccaagccgcttgccagaaagctgcgccccgcccaaa agcactgggttctgcagtccaggcccttcctcagctcccaggtccaggag aactgcaaggtcacctacttccacaggaagcactgggtccgcatccggcc cctccgcaccactcctcccagctgggactacacccgcatctgcatccaga gagagatggtccccgcccgcatccgcgtcctgagagagatggtccccgag gcctggaggtgctttcccaacaggctgccgctgctgagcaacatcaggcc tgatttctccaaggctcccctggcctacgtgaagcggtggctttggaccg cccgccacccccacagcctgtccgcagcctggtgaccgtgaaaatcgccc cgccagagagcagaggaagcccgacgcccaggccatctgccttcaggtct gtgatgagaaacggagtggcctgttccgttgtgcccaggtctaggccgct gagcagagccctcactcccaggcagagttgtctgaatccttcct &gt;NM_181640 2 atgcgcgcaagagagcgggaagccgagctgggcgagaagtaggggagggc ggtgctccgccgcggtggcggttgctatcgcttcgcagaacctactcagg cagccagctgagaagagttgagggaaagtgctgctgctgggtctgcagac gcgatggataacgtgcagccgaaaataaaacatcgccccttctgcttcag tgtgaaaggccacgtgaagatgctgcggctggatattatcaactcactgg taacaacagtattcatgctcatcgtatctgtgttggcactgataccagaa accacaacattgacagttggtggaggggtgtttgcacttgtgacagcagt atgctgtcttgccgacggggcccttatttaccggaagcttctgttcaatc ccagcggtccttaccagaaaaagcctgtgcatgaaaaaaaagaagttttg taattttatattactttttagtttgatactaagtattaaacatatttctg tattcttccacatattttctgcagttattttaactcagtataggagctag aggaagagatttccgaagtctgcaccccgcgcagagcactactgtaactt ccaagggagcgctgggagcagcgggatcgggttttccggcacccgggcct gggtggcagggaagaatgtgccgggatccgcctcagggatctttgaatct ctttactgcctggctggccggcagctccg &gt;NM_016951 3 atgcgcgcaagagagcgggaagccgagctgggcgagaagtaggggagggc ggtgctccgccgcggtggcggttgctatcgcttcgcagaacctactcagg cagccagctgagaagagttgagggaaagtgctgctgctgggtctgcagac gcgatggataacgtgcagccgaaaataaaacatcgccccttctgcttcag tgtgaaaggccacgtgaagatgctgcggctggcactaactgtgacatcta tgaccttttttatcatcgcacaagcccctgaaccatatattgttatcact ggatttgaagtcaccgttatcttatttttcatacttttatatgtactcag acttgatcgattaatgaagtggttattttggcctttgcttgatattatca actcactggtaacaacagtattcatgctcatcgtatctgtgttggcactg ataccagaaaccacaacattgacagttggtggaggggtgtttgcacttgt gacagcagtatgctgtcttgccgacggggcccttatttaccggaagcttc tgttcaatcccagcggtccttaccagaaaaagcctgtgcatgaaaaaaaa gaagttttgtaattttatattactttttagtttgatactaagtattaaac atatttctgtattcttccacatattttctgcagttattttaactcagtat aggagctagaggaagagatttccgaagtctgcaccccgcgcagagcacta ctgtaacttccaagggagcgctgggagcagcgggatcgggttttccggca cccgggcctgggtggcagggaagaatgtgccgggatccgcctcagggatc tttgaatctctttactgcctggctggccggcagctccg &gt;NR_002773 1 cagcaccacaccaggaccctccagaggctgtgagaaacatcctgcaccca ggtcctctctatctgtttatcattgtctattttgtattctgcattcagaa ccaagagcctgaagacgacccaggagctttagctatggctgtcttcatta ttttgtccctgtttagtgttctggtgacaggcatgggtgaaggtggggct gggagtgagaaaggaggtgagagggaatgtaagctgaaccagcttcccca ttgcccctccgtatctcccagtgcccagccttggacacaccctggccaga gccagctgtttgcagacctgagccgagaggagctgacggctgtgatgcgc tttctgacccagcagctggggccagggctggtggatgcagcccaggccca gccctcggacaactgtgtcttctcagtggagttgcagctgcctcccaagg ctgcagccctggctcacttggacagggggagccccccacctgcccgggag gcactggccatcgtcttctttggcaggcaaccccagcccaacgtgagtga gctggtggtggggccactgcctcacccctcctacatgcgggacgtgactg tggagcgtcatggaggccccctgccctatcaccgacgccccatgttgttc caagagtacctggacatagaccagatgatcttcgacagagagctgcccca ggcttctgggcttctccatcactgttgcttctacaagcgccggggacgga acctggtgacaatgaccacggctccccgtggtctgcaatcaggggaccgg gccacctagtttggcctctactacaacatctcgggcgctgggttcttcct gcaccacgtgggcttggagctgctagtgaaccacaaggcccttgaccctg cccgctggactatccagaaggtgttctatcaaggccgctactatgacagc ctggcccagctggaggcccagtttgaggccggcctggtgaatgtggtgct gatcccagacaatggcacaggtgggtcctggtccctgaagtcccctgtgc ccccgggtccagctccccctctgcagttccatccccaaggcccccgcttc agtgtccagggaagtcgagtggcctcctcactgtggactttctcctttgg cctcggagcattcagtggcccaaggatctttgacgttcccttccaagggg agagggtggcctatgaagtcagtgtccaggcggccttggccatctatgga ggcaattctccttctgctctacgaagccggtacatagatagtggctttgg cttgggccacttctccacgcccctgacccatggggtggactgcccctacc tggccacctacgtggactggcacttcctttttgagtcccaggccgccaag acaatacgcgatgccttttgtatatttgaacagaaccagggcctccccct gcggcgacaccactcagatctctactcccactactttgggggccttgcgg aaacggtgctggtcatcagatctgtgtctactatgctcaactatgactat gtgtgggatatggtcttccaccctaatggggccatagaaatcagactcca caccaccggctacatcagctcagcattcccctttggtgctgcccagaggt atggaaacaaagtttcagagcacaccctgggcacggtccacacccacagc gcccacttcaaggtggacctggatgtagcaggtaaggcatcctggcagag gcaaaagtgctggaggggtgagctgaagtctccatgcctagctttaaaag ttttcgttgggctgggagcagtagcttatgcctgtaagcccaacactttg ggagactgaggggggtggatcacttgaggtcaggagttcaaaaccagcct ggccaacatggcgaaatcctgtctgtactaaaaatacaaaaattagctgg gcatgggtatgctgtaatcctagctactcgggaggctgaggcaggagaat cacttgaatctgggagtcagaggttgcagtgagctgagattgagccactg cactccatcctgcgtgactgaac &gt;NR_037806 1 attcccagtcacccactcactcagaaagccgggagtcatcggacaccttg ctggtcagaggtcctgggggtggttttgaaccatcagagcttggactttt ctgacttccccagcaaggatcttcccacttcctgctccctgtgttcccac cctccagtgttggcacaggcccacccctggctccaccagagccagaagca gaggtagaatcaggcgggccccgggctgcactccgagcagtgttcctggc catctttgctactttcctagagaacccggctgttgccttaaatgtgtgag agggacttggccaaggcaaaagctggggagatgccagtgacaacatacag ttcatgactaggtttaggaattgggcactgagaaaattctcaatatttca gagagtccttcccttatttgggactcttaacacggtatcctcgctagttg gttttaagggaaacactctgctcctgggtgtgagcagaggctctggtctt gccctgtggtttgactctccttagaaccaccgcccaccagaaacataaag gattaaaatcacactaataacccctggatggtcaatctgataataggatc agatttacgtctaccctaattcttaacattgcagctttctctccatctgc agattattcccagtctcccagtaacacgtttctacccagatcctttttca tttccttaagttttgatctccgtcttcctgatgaagcaggcagagctcag aggatcttggcatcacccaccaaagttagctgaaagcagggcactcctgg ataaagcagcttcactcaactctggggaatgctaccattttttttccaaa gtagaaaggaagcacttctgagccagtgaccactgaaagatgaacactct tcctgatcctctcctctagaattcatctcctcctgctagcagccgcgtcc tggaggagcagcggatggggaatccattctgtttcttcctggtgtttagg aagttgccccacacacagattgccccgatgtccaaccagaagaagtgaaa ctgctgctgggtctggagaggtgaagacccgtggccagcttctgttgttg ccatcggccattgctttttgttcgcttgcttttggttttgcaagaagagc ggcctctgtctctgatctgcttcaaatcatcattccatcagtgacagaag tggctgttccatcagtggtcgcagccagttcagctcctgcatccatcccc aagtgttctgagtggaatttgaggcctccccaaccacctaccaaaaaagg agggtgaaatgaaaggaagaagaaaaactcagcattctttcctctgacaa agagtaaaacgacaaggaatatcggcctgaattctcttcccaagaagaaa gaaagcacaccaacgcaggcatttgtcttctgtccatggtgctgaagttt attcactttcaaaccactttcagtaacagcaaattctttagaaaaggaaa atacagggaaagggataaacctcactgacttggaggaaatcaagaggagt gagcacagcatcagaaagccccctggccccagactgcacccgctttcctg gccctaccttgaaatccatcaggtctgcgttggacacggcattgtacatg ggattagctctg </code></pre> <p>Any help and input would be deeply appreciated. </p> <p>Thank you for taking the time to go through my problem!</p>
    singulars
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      1. POPerl: Search a pattern across array elements
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    2. VO
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    1. COAre you sure you don't want `my $npat = '[A-FH-Z]{1,25}'`? i.e. can the sequences between the `G`s really also contain `G`s? The two alternatives give very different results.
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      1. USBorodin
    2. CO@Borodin Hello again sir! Indeed the sequences between the Gs can also contain 1-2 Gs. So 'my $npat' would indeed be '[A-Z],{1,25}'. The $pattern is a very special motif found in our DNA and RNA sequences and have been recently discovered to have great significance in regulating basic biological phenomenon like expression of genes etc
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      1. POPerl: Search a pattern across array elements
      1. USNeal
 

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