Size of the match without gaps in BlastN

Question

[samuelmiver]

I am locating specific sequences in a genome using BlastN. The sequences (47 nucleotides of total length) include (after a filtering process) 32 original nucleotides and 15 bases of a sequence that does not appear in the genome coming from a transposon insertion.

My intention is to give to blast the condition that it has to be 32 nucleotides matching the genome in the same alignment block. I do not find this concrete option but maybe an expert in blast could achieve the same results playing with the open and extension gap costs.

Thank you very much in advance.

[lieven.sterck]

How are these nucleotides 'organised', is it like a stretch of matching bases and a stretch of non-matching? Is it 100% matching or can there be mismatches/gaps as well?

Answer 1

[sapoudel]

I believe you are looking for the '-word_size' argument. See details below:

http://www.metagenomics.wiki/tools/blast/default-word-size

From the link: "A BLAST search starts with finding a perfect sequence match of length given by -word_size. This initial region of an exact sequence match is then extended in both direction allowing gaps and substitutions based on the scoring thresholds."