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FASTA-type searches with customized subset of dat

Christoph Gartmann GARTMANN at IMMUNBIO.MPG.DE
Sat Dec 17 13:10:51 EST 1994


In <vuilleumier.58.000F596D at micro.biol.ethz.ch> vuilleumier at micro.biol.ethz.ch writes:

> I have a set of fingerprint  motifs (Prosite, Prints) of interest which 
> include the accession numbers  of all proteins which have such a motif. 
> Can I do a FASTA-type search on a file containing just the accession numbers 
> of these proteins?
> Or do I have to  all  these sequences (hundreds) from the databases 
> with FETCH, give them names, put these names in a file, use this file to do 
> FASTA? In this case, can I automate the fetch process?

When your are prompted for the sequences to scan just enter something like
   @my_file.name
Note the "@" preceding your filename to indicate that your file is a
"file of sequence names". And it shouldn't matter whether it contains
real sequence names or just accession numbers.

Regards,
   Christoph Gartmann


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