[EMBOSS] Netblast search of swissprot and trembl......

[Jon Ison]

Hi Richard

seqret can read a "list file" which is a list of USAs (one per line).
A USA (Uniform Sequence Address) is the EMBOSS method of specifying
sequences from databases, files etc.  You'll need the "@myfile" or
"list::myfile" syntax where "myfile" is the file name of your list
of sequences.  You can output in all the common formats.

Read the documentation :
http://emboss.sourceforge.net/apps/seqret.html

Cheers

Jon



> I am using blastcl3 to search NCBI using multiple bait sequences in
> fasta format. I can readily search swissprot using this program, but
> cannot search trembl. The NCBI accession numbers (ie just numbers) that
> blastcl3 returns require re-labelling of the sequences to make clustal
> outputs, phylogeny analyses etc. meaningful.
>
>
>
> Is there an easily-installed linux client that can search trembl? Can
> blastcl3 be forced to do it?
>
>
>
> What I would like to do is feed seqret a file containing the trembl
> accessions. This would generate a fasta file with more meaningful titles
> comprising the accession number followed by the swissprot organism
> abbreviation.
>
>
>
> Thanks,
>
>
>
> Richard
>
>
>
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