generate a FASTA file with a annotation file (extension .dat)

[Peter Rice]

julien Faurie wrote:
> I downloaded swissprot release and now, I would like to generate my
> fasta file.
> 
> In EMBOSS documention, I found the command "seqret"

Good choice. You can pick the fasta format you prefer:


% seqret seq.dat -sformat swissprot swissprot.fasta

... gives you fasta headers like this:

 >100K_RAT Q62671 100 KDA PROTEIN (EC 6.3.2.-).

% seqret seq.dat -sformat swiss swissprot.ncbi -osformat ncbi

... gives you fasta headers like this:

 >gnl|unk|100K_RAT (Q62671) 100 KDA PROTEIN (EC 6.3.2.-).

% seqret seq.dat -sformat swiss swissprot.blast -osformat ncbi -osdbname sp

... gives you fasta headers like this:

 >gnl|sp|100K_RAT (Q62671) 100 KDA PROTEIN (EC 6.3.2.-).

Note in passing ... it seems 100K_RAT is no longer the first entry in 
SwissProt, as accession Q62671 is now called KC11_RAT (Casein Kinase I 
gamma 1 isoform).

-- 
------------------------------------------------
Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723