NCBI fasta format [was: Re: [Bioperl-l] loading data into bioperl-db]

Aaron J Mackey ajm6q at
Fri Jun 6 22:37:05 EDT 2003

On Fri, 6 Jun 2003, Hilmar Lapp wrote:

> The advantage is you can modify and tweak it easily at any time and plug
> it back in (no make / install or messing with perl libraries), and you
> can use it for any format, not just fasta.

Right; the SeqProcessor route is very powerful, and can easily handle this
task.  But isn't that overkill for this?  I thought that this "bundled id"
NCBI uses only shows up in the fasta files they generate (so using it for
other formats is a moot point).  A Bio::SeqIO::fasta_ncbi (or some other,
better name) would be simple for beginners, and would be useful for
Bio::DB::GenBank as well (that is, if Bio::DB::GenBank still requests
fasta-formatted data from Entrez).


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