Accession List from Blast output? (Was: Re: [Bioclusters] Seqret)

[Nick Brockner]

Hi Simon,

Thanks for the pointers.  My nt database is segmented into 512 MB 
chunks.  I have found that the NCBI "fastacmd" command will do for now. 
  I do, however, have one more question:

Does anyone know how one would go about getting output which contains 
only a list of accession numbers of the matching sequeces from running 
a Blastp?

Thanks,

Nick

> By any chance is the file which contains U51243 > 2Gb in size?  The
> current version of dbiflat fails to index any sequences past the 2Gb
> limit in any file and just silently drops them.
>
> There is a fix in the works in the next EMBOSS release, but for now the
> only fix is to split your database files into <2Gb chunks.
>
> If this isn't it, try running seqret -debug nt:U51243 and look at the
> seqret.dbg file for clues as to what's going wrong.
>
> Simon.