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Blast Params : Word Size, Gap Existence, Extension Penalties

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.

biopython python blast
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updated by brentp brentp • written by Adi • Adi

1 answer

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")
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updated by Ram Ram • written by brentp brentp

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