Stand alone balst+

Question

[hemantcnaik]

I am doing stand alone blast i want set query coverage, how to get the query best hists above 60%

[GenoMax]

Have you looked at the format options for NCBI blast. Especially qcov option in outfmt.

[hemantcnaik]

my query file vary with sequence size result all so showing less coverage to that sequence i am no getting proffer result to sequence simlarity

Answer 1

[h.mon]

You may filter after blasting, if you use genomax suggestion, or you may use the -qcov_hsp_perc parameter (you may also want to use -max_hsps):

-qcov_hsp_perc <real, 0..100="">
Percent query coverage per hsp