Hello, Pon. We have resolved this issue with "Max hits" for local BLASTs. The solution is available in our development snapshots:
http://ugene.unipro.ru/snapshot.html (revision 7662 or greater).
But we have found that the name of this option is incorrect.
The problem is that local BLASTs does not have the option "HITLIST_SIZE" that is used in the remote BLAST. And we try to emulate this option for local BLAST+ with another one:
Quote:-culling_limit <Integer, >=0>
If the query range of a hit is enveloped by that of at least this many
higher-scoring hits, delete the hit
This option helps with reducing the results amount but it is not that limit of results provided by the remote BLAST.
Could you help us with improving this area of UGENE? How do you think what solution is better?
1) The current one is good, we don't need to change something.
2) We need to rename the "Max hits" option for BLAST+ according to the -culling_limit description because this option is not the same as for the remote BLAST.
3) We need to leave this name for the option, but change its implementation: take only first "Max hits" results of BLAST+ and throw away other results.
I think that the solution #3 is the best, but I don't know if it is correct to just cut the results. I don't know if the results are sorted by its some "best" characteristic or something like that.
Do you know the answers for these questions?
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