[Bioperl-l] Fasta sequence width question

Brian Osborne bosborne11 at verizon.net
Wed Feb 22 16:50:58 EST 2012


Francis,

There's has never been a decision, to my knowledge, to base "global" Bioperl defaults on NCBI's conventions. Yes, there are tools in Bioperl that access NCBI in various ways but Bioperl does not generally refer to NCBI for its definitions.

Brian O.

On Feb 22, 2012, at 4:37 PM, Francisco J. Ossandón wrote:

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




More information about the Bioperl-l mailing list