Dear EMBOSS users,
I am new to protein profile searches and am using prophecy and prophet
for a distant similarity search. I'm trying to use BLOSUM45, but prophet
is reporting BLOSUM62.
I'm generating profiles using prophecy and the BLOSUM45 matrix, thus:
prophecy -auto -warning -type H -datafile EBLOSUM45 -name
homologene_1825.aln -outfile homologene_1825.prophecy
This seems fine.
I'm using the profiles to search a protein database, thus:
prophet -auto -warning -infile homologene_1825.prophecy -outfile
prophet_out.txt -sequence
NC_000909_Methanocaldococcus_jannaschii_DSM_2661_prots.fasta
I am puzzled by this line I get in my prophet output (prophet_out.txt in
this case):
# Matrix: EBLOSUM62
I can't seem to make it go away. The profile file itself
(homologene_1825.prophecy) does correctly report BLOSUM45:
Matrix EBLOSUM45
Is there any way to make prophet also use BLOSUM45? (Does it in fact
make any difference to prophet?)
Thank you very much for advice.
Best regards,
Daniel
--
Daniel Barker
http://bio.st-andrews.ac.uk/staff/db60.htm
The University of St Andrews is a charity registered in Scotland :
No SC013532
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