From blastx web page, the option "Max matches in a query range" is described as "Limit the number of matches to a query range. This option is useful if many strong matches to one part of a query may prevent BLAST from presenting weaker matches to another part of the query. The algorithm is based upon an article called "Winnowing sequences from a database search."
I have long sequences to blastx and the goal is to "walk along the sequence" and output the best blast hits. This isn't possible if you have a very high scoring hit in a conserved region (e.g. bacteria). All you get are hits from that region only. For example, the following is what I am aiming at. With "regular" blast, the first hit takes all room there is.
gi_number start end score 693061703 14 2137 1428 903595944 2617 3324 484 26107643 4785 3931 548 928870515 5740 4739 595 693076326 7321 6371 656
NCBI website allows the "walk along the sequence" approach with the "Max matches in a query range" option (the output above; parameter is set to 1). It works beautifully! I am trying to do this within standalone blast. There is a similar question, but nobody answered it properly. I have tried the following parameters, but failed to get the above every time:
-max_hsps 1 -max_target_seqs 1 -max_target_seqs 10