[Bioclusters] Help on BLAST
Chaopeng
bioclusters@bioinformatics.org
Thu, 22 Aug 2002 12:40:10 -0400
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Dear Dr. Glen,
I am new to blast and am currently comparing the MPI version of blast =
search (wrapped by myself) and the openMosix approach. I read some post =
saying the blast patch for openMosix makes the search 20% slower. I want =
to know whether I can get better performance with MPI.
I read your posts saying "splitting the query sequence into small =
fragments and BLASTing each of those fragments against the (entire) =
database is super-easy to implement." Could you please tell me how to =
combine the results, or a link to the solution would be very helpful?
Thanks for your time and assistance.
Sincerely,
Chaopeng Zhou
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Chaopeng Zhou
Department of Computer Science & Engineering
U-3155,
The University of Connecticut,
Storrs, CT 06269
tel: (860) 486-3309
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<DIV><FONT face=3DArial>Dear Dr. Glen,</FONT></DIV>
<DIV><FONT face=3DArial></FONT> </DIV>
<DIV><FONT face=3DArial>I am new to blast and am currently comparing the =
MPI=20
version of blast search (wrapped by myself) and the openMosix =
approach. I=20
read some post saying the blast patch for openMosix makes the=20
search 20% slower. I want to know whether I can get better =
performance with=20
MPI.</FONT></DIV>
<DIV><FONT face=3DArial></FONT> </DIV>
<DIV><FONT face=3DArial>I read your posts saying "splitting the query =
sequence=20
into small fragments and BLASTing each of those fragments against the =
(entire)=20
database is super-easy to implement." Could you please tell me how to =
combine=20
the results, or a link to the solution would be very =
helpful?</FONT></DIV>
<DIV><FONT face=3DArial></FONT> </DIV>
<DIV><FONT face=3DArial>Thanks for your time and =
assistance.</FONT></DIV>
<DIV><FONT face=3DArial></FONT> </DIV>
<DIV><FONT face=3DArial>Sincerely,</FONT></DIV>
<DIV><FONT face=3DArial>Chaopeng Zhou</FONT></DIV>
<DIV><FONT face=3DArial></FONT> </DIV>
<DIV><FONT face=3DArial=20
size=3D2>----------------------------------------------------------------=
-----------<BR>Chaopeng=20
Zhou<BR>Department of Computer Science & =
Engineering<BR>U-3155,<BR>The=20
University of Connecticut,<BR>Storrs, CT 06269<BR>tel: (860)=20
486-3309<BR>-------------------------------------------------------------=
--------------</FONT></DIV></BODY></HTML>
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