[Bioperl-l] length of hit->description

[Smithies, Russell]

You beat me to it ☺
Even fasta36 truncates the description – which running fasta from the command-line would have shown you straight away.
Eg.

intrepid$ fasta36 -b1 MyORF.tfa  test.fna
# fasta36 -b1 MyORF.tfa test.fna
FASTA searches a protein or DNA sequence data bank
version 36.3.5c Dec, 2011(preload8)
Please cite:
W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448

Query: MyORF.tfa
  1>>>test - 39 aa
Library: test.fna
       93 residues in     1 sequences

Statistics: (shuffled [495]) MLE statistics: Lambda= 0.1960;  K=0.09883
statistics sampled from 1 (1) to 495 sequences
Algorithm: FASTA (3.7 Nov 2010) [optimized]
Parameters: BL50 matrix (15:-5), open/ext: -10/-2
ktup: 1, E-join: 1 (1), E-opt: 0.2 (1), width:  16
Scan time:  0.040

The best scores are:                                      opt bits E(1)
gi|20800434|ref|NP_620820.1| putative DNA-binding  (  93)  193 58.0 1.2e-14

>>gi|20800434|ref|NP_620820.1| putative DNA-binding repl  (93 aa)
initn: 157 init1: 157 opt: 193  Z-score: 295.2  bits: 58.0 E(1): 1.2e-14
Smith-Waterman score: 193; 87.2% identity (87.2% similar) in 39 aa overlap (6-39:55-93)

                                        10        20             30
test                            MPAENQGMKYREIAEEMEISTGAVGRL-----KHD
                                     ::::::::::::::::::::::     :::
gi|208 RTIRNIVAESRDSYQARAAERRDTAVKLREQGMKYREIAEEMEISTGAVGRLLHDAKKHD
           30        40        50        60        70        80



--Russell



From: bioperl-l-bounces+russell.smithies=agresearch.co.nz at mailman.open-bio.org [mailto:bioperl-l-bounces+russell.smithies=agresearch.co.nz at mailman.open-bio.org] On Behalf Of Torsten Seemann
Sent: Friday, 25 July 2014 8:10 a.m.
To: Antony03
Cc: Bioperl-l at mailman.open-bio.org
Subject: Re: [Bioperl-l] length of hit->description

my $fasta   = 'fasta35';

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.
http://faculty.virginia.edu/wrpearson/fasta/fasta36/

my $command = "$fasta -b 1 $query $library";

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").

--
--Torsten Seemann
--Victorian Bioinformatics Consortium, Dept. Microbiology, Monash University, AUSTRALIA
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