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
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