[Mpiblast-users] Seed Size in mpiformatdb?

[Hansen, Raymond A]

Title: Seed Size in mpiformatdb?

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