[Bioperl-l] Fasta sequence width question

Chris Fields cjfields at illinois.edu
Wed Feb 22 17:42:04 EST 2012


No reason, beyond legacy and possibly a fear that changing it could 
cause unforeseen consequences down the road.

chris

On 02/22/2012 03:37 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
>>
>>
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>> Bioperl-l at lists.open-bio.org
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>
>
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