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.
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written
by
samuelmiver
1 answer
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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