[Bioperl-l] Fasta sequence width question

Francisco J. Ossandón fossandonc at hotmail.com
Wed Feb 22 13:55:23 EST 2012


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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