Thanks for the response Michael. I apologize. I failed to mention that my group is requiring the use of mpiblast, if at all possible. What arguements could one make for the use of NCBI BLAST over mpiBLAST? The information in the link you provided looks like it is starting to get at some of the performance/evaluation criteria that the group is interested in observing. I think this brings up a few more questions for me. For a matter of my own understanding, is it correct that the database must be formatted to that word size? If so, wouldn't it increase accuracy and performance if the database word size matches the size of the word size specified at the command line invocation of mpiBLAST? Next, will NCBI BLAST run on cluster? I am under the impression that mpiblast is simply the parallelized version of BLAST. Finally, Will the use of the -W parameter in mpiBLAST [instead of NCBI BLAST] cause any issues for an alignment where the database isn't formatted with the same word length? I have a feeling that the O'Reilly book and I are going to be spending alot of quality time together over the next few days. Thanks, -Ray
________________________________ From: [EMAIL PROTECTED] on behalf of Michael Cariaso Sent: Mon 2/6/2006 9:22 PM To: [email protected] Subject: Re: [Mpiblast-users] Seed Size in mpiformatdb? What you're describing sounds like the 'word size' setting in ncbi blast. This is controlled with the -W setting. http://www.ncbi.nlm.nih.gov/Web/Newsltr/Spring00/blastlab.html If this sounds like what you are looking for you probably only need ncbi blast, not mpiblast. O'Reilly & Associates has a good reference book "BLAST" which might be helpful. Hansen, Raymond A wrote: > > Hello All, > > I am fairly new to the world of BLAST, so please forgive my ignorance. > I have searched the archives and have not found anything related to my > needs. > > First, as I understand it at a high level, mpiformatdb takes the > database specified and divides it into the desired number of segments. > Within each of these segments it also "indexes" the database into > sequential 11 nuecleotide sequences called seeds/words/indexes (?). > These seeds are then used during the alignment [mpiblast] to identify > sequences with a high likelihood of a match. > > My question is this: Is it possible [or even feasible] to change the > number of bases in each seed? The Bio/Genomic group that I am working > with has a desire to explore alignments utilizing different seed > lengths, and I don't have a solid grasp for the underlying code. > > Any assistance would be greatly appreciated, > > -Ray > ------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121642 _______________________________________________ Mpiblast-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mpiblast-users
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