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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">You beat me to it
</span><span style="font-size:11.0pt;font-family:Wingdings;color:#1F497D">J</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Even fasta36 truncates the description – which running fasta from the command-line would have shown you straight away.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Eg.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New"">intrepid$ fasta36 -b1 MyORF.tfa test.fna<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New""># fasta36 -b1 MyORF.tfa test.fna<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New"">FASTA searches a protein or DNA sequence data bank<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New"">version 36.3.5c Dec, 2011(preload8)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New"">Please cite:<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New"">W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New"">Query: MyORF.tfa<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New""> 1>>>test - 39 aa<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New"">Library: test.fna<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New""> 93 residues in 1 sequences<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New"">Statistics: (shuffled [495]) MLE statistics: Lambda= 0.1960; K=0.09883<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New"">statistics sampled from 1 (1) to 495 sequences<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New"">Algorithm: FASTA (3.7 Nov 2010) [optimized]<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New"">Parameters: BL50 matrix (15:-5), open/ext: -10/-2<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New"">ktup: 1, E-join: 1 (1), E-opt: 0.2 (1), width: 16<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New"">Scan time: 0.040<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New"">The best scores are: opt bits E(1)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New"">gi|20800434|ref|NP_620820.1| putative DNA-binding ( 93) 193 58.0 1.2e-14<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New"">>>gi|20800434|ref|NP_620820.1<span style="background:yellow;mso-highlight:yellow">| putative DNA-binding repl</span> (93 aa)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New"">initn: 157 init1: 157 opt: 193 Z-score: 295.2 bits: 58.0 E(1): 1.2e-14<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New"">Smith-Waterman score: 193; 87.2% identity (87.2% similar) in 39 aa overlap (6-39:55-93)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New""> 10 20 30<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New"">test MPAENQGMKYREIAEEMEISTGAVGRL-----KHD<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New""> :::::::::::::::::::::: :::<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New"">gi|208 RTIRNIVAESRDSYQARAAERRDTAVKLREQGMKYREIAEEMEISTGAVGRLLHDAKKHD<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt;font-family:"Courier New""> 30 40 50 60 70 80<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Courier New";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">--Russell<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> bioperl-l-bounces+russell.smithies=agresearch.co.nz@mailman.open-bio.org
[mailto:bioperl-l-bounces+russell.smithies=agresearch.co.nz@mailman.open-bio.org]
<b>On Behalf Of </b>Torsten Seemann<br>
<b>Sent:</b> Friday, 25 July 2014 8:10 a.m.<br>
<b>To:</b> Antony03<br>
<b>Cc:</b> Bioperl-l@mailman.open-bio.org<br>
<b>Subject:</b> Re: [Bioperl-l] length of hit->description<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">my $fasta = 'fasta35';<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Firsly, I would recommend upgrading to fasta36 which was released in 2011 I think. It's focussed on batch and command line usage rather than interactive usage.<o:p></o:p></p>
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<p class="MsoNormal"><a href="http://faculty.virginia.edu/wrpearson/fasta/fasta36/">http://faculty.virginia.edu/wrpearson/fasta/fasta36/</a><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">my $command = "$fasta -b 1 $query $library";<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">By default fasta36 truncates the descriptions (and I think fasta35 did too), so I think you need to add "-L" to the options ("long library descriptions").<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">-- <br>
--Torsten Seemann<br>
--Victorian Bioinformatics Consortium, Dept. Microbiology, Monash University, AUSTRALIA<o:p></o:p></p>
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