Size of the match without gaps in BlastN
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7.1 years ago
samuelmiver ▴ 440

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.

sequencing blast • 2.0k views
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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?

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3.4 years ago
sapoudel • 0

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."

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