Question: Winnowing sequences in blast search
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gravatar for Kate
4.0 years ago by
Kate20
United States
Kate20 wrote:

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

Any idea?

blast sequence alignment • 1.0k views
ADD COMMENTlink modified 17 months ago by RamRS25k • written 4.0 years ago by Kate20
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