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What is the effect of Best_hit_overhang and Best_hit_score_edge on number of subject HSPs in blast+?

I can't find a detailed description of these two flags -best_hit_overhang and -best_hit_score_edge.

I would like to limit the number of HSPs in my tblastn output (as several threads seem to have aimed to do). Limiting targets/subject sequences is easy enough, but the remaining multiple HSPs within each hit is not what I want.

Is there a function to maximise HSP coverage and to only output this HSP, without strictly limiting the number of HSP outputs to 1 (-max_hsps 1) or else pulling out the best scoring HSPs by line by some script.

-qcov_hsp_perc seems like it may be relevant (Percent query coverage per hsp, 0..100). If set to 100, would the output HSPs of the subject/hit only be those with 100pc coverage of the query?

blast sequence alignment
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updated by Biostar Biostar • written by oliver.bayfield • oliver.bayfield

1 answer

-qcov_hsp_perc does exactly what you think it does. However, it says it takes a float so if you want 100% coverage I would try both and see which gives the desired results:

-qcov_hsp_perc 1.0 

-qcov_hsp_perc 100
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written by tlawrence3 • tlawrence3

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