[Bioperl-l] Fasta sequence width question

[Francisco J. Ossandón]

Yes, I know about the method to change the width myself, thanks. =)
My question was more about if there was an specific reason to choose that
default value (60) instead of the NCBI value (70). And if it should be
changed to 70 to match NCBI or not.

Cheers,
 
Francisco J. Ossandon

-----Mensaje original-----
De: bioperl-l-bounces at lists.open-bio.org
[mailto:bioperl-l-bounces at lists.open-bio.org] En nombre de Brian Osborne
Enviado el: miércoles, 22 de febrero de 2012 16:28
Para: Francisco J. Ossandón
CC: Bioperl-l at lists.open-bio.org
Asunto: Re: [Bioperl-l] Fasta sequence width question

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
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


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