[Bioperl-l] Parsing FASTA m10 output

Chris Fields cjfields at uiuc.edu
Mon Apr 23 08:46:40 EDT 2007

That's true, but older versions of fasta don't do this.  For  
instance, the example files in the bioperl distribution in t/data  
(HUMBETGLOA.FASTA, cysprot1.fasta, cysprot_vs_gadfly.fasta) lack this  

 From the fasta changelog:

 >>Nov 14-22, 2002  CVS fa34t20b6

Include compile-time define (-DPGM_DOC) that causes all the fasta
programs to provide the same command line echo that is provided by the
PVM and MPI parallel programs.  Thus, if you run the program:

     fasta34_t -q -S gtt1_drome.aa /slib/swissprot 12

the first lines of output from FASTA will be:

     # fasta34_t -q gtt1_drome.aa /slib/swissprot
      FASTA searches a protein or DNA sequence data bank
      version 3.4t20 Nov 10, 2002
     Please cite:
      W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448

This has been turned on by default in most FASTA Makefiles.

We could only support newer fasta output (newer that the above  
version) since there have been several bug fixes and changes to  
output; not sure how everyone else feels about this.


On Apr 23, 2007, at 4:45 AM, Ioannis Kirmitzoglou wrote:

> I don't know about older versions but the latest version of FASTA  
> starts its
> output with a line similar to those:
> # fasta34.exe -m9 -d0 -Q test.faa test.faa OR
> # fasta34.exe -m10 -Q test.faa test.faa
> This very first line is also the only one in the output that starts  
> with
> '#'.
> Isn't this an easy way to determine the output type?
> -- 
> *Ioannis Kirmitzoglou*, MSc
> PhD. Student,
> Bioinformatics Research Laboratory
> Department of Biological Sciences
> University of Cyprus
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign

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