Blast Params : Word Size, Gap Existence, Extension Penalties

Question

[Adi]

I have just started Biopython and require some assitance. Using 'NCBIWWW.qblast' function (or any other); how can I set the word size and gap existence,extension penalties for BLASTp? Thanx in advance.

Answer 1

[brentp]

Have a look at the function signature. kwargs are:

word_size gapcosts (for gap open, extend in spaced format: http://www.ncbi.nlm.nih.gov/BLAST/Doc/node28.html)

so example invocation is:

>>> from Bio.Blast import NCBIWWW
>>> NCBIWWW.qblast('blastp', 'nr', open('seqs.fa').read(), word_size=10, gapcosts="10 3")