BLAST/FASTA search of a specific sequence

Dr Mick Jones mjones at rpms.ac.uk
Mon Oct 16 09:53:05 EST 1995


Hi netters

I am hoping that somebody out there can help me.

What I want to do is search all 6 possible orfs of specific sequences 
with a very short peptide sequence (6 - 10 aa in length).  The specific 
sequences are the complete sequences of human herpesviruses, each one is 
>150,000 bp in size.

If I send to a server to do a BLAST/FASTA search of the EMBL or GenBank 
databases I will probably have to sift through lots of irrelevant 
matches.

Anybody out there got a solution.

Many thanks

Mick

_____________________________________________________________________
Mick Jones                      Tel: 081-740-3328 (+44-81-740-3328)
Department of Virology          FAX: 081-743-8331 (+44-81-743-8331)
RPMS,  Du Cane Road              Email: mjones at rpms.ac.uk 
London,  W12 0NN,  UK          URL: http://www.rpms.ac.uk/rpms_home.html
***********************************************************
"Smoke me a kipper, I'll be back for breakfast."   Ace Rimmer (Red 
Dwarf)
"Crackin' bit of toast, Gromit."    Wallace (The Wrong Trousers)
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