FASTA-type searches with customized subset of database?

[Stephane Vuilleumier]

Hi, 
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?

Thanks for any suggestions!
Stephane
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Stephane Vuilleumier
Mikrobiologisches Institut
ETH-Zurich
ETH-Zentrum/LFV                       Phone:  (+41) 1 632 33 57
8092 Zurich                           Fax:    (+41) 1 6