[Bioperl-l] Fasta sequence width question

Brian Osborne bosborne11 at verizon.net
Wed Feb 22 14:28:12 EST 2012


Francis,

You can set this yourself.

http://search.cpan.org/~cjfields/BioPerl-1.6.901/Bio/SeqIO/fasta.pm#width

Brian O.


On Feb 22, 2012, at 1:55 PM, Francisco J. Ossandón wrote:

> Hello,
> I have a question about the width used by Bioperl in the Fasta format. This
> format recommends that lines of text be shorter than 80 characters, but
> there is no really fixed length for the sequence lines.
> http://en.wikipedia.org/wiki/FASTA_format
> http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml
> 
> I usually download sequences from NCBI and their Fasta sequences always use
> a sequence line width of 70 characters (like
> http://www.ncbi.nlm.nih.gov/protein/50842445?report=fasta ), while Bioperl
> uses a default of 60 to write in Fasta format using Bio::SeqIO::Fasta
> ("BEGIN { $WIDTH = 60}"). Is there a particular reason to set the width at
> 60 characters?? Or maybe it could be changed to 70 to match NCBI??
> 
> Cheers,
> 
> Francisco J. Ossandon
> 
> 
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