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Workflow Designer - Local blast- max hits (Read 10415 times)
Jun 12th, 2014 at 6:17pm

pon   Offline
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Posts: 4
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Hi,

I'd like to see the option max-hits for the "Local Blast+ Search"  in the Workflow-Designer. It is not very comfortable to get 100 results, the abilty to limit the results as in the remote Blast function would be very helpful.

Regards,
pon
 
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Reply #1 - Jun 15th, 2014 at 2:32pm

Olga Golosova   Offline
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Posts: 338
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Hi Pon!

Sure, we will add the parameter, thanks for the request!

Regards,
Olga

 
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Reply #2 - Sep 16th, 2014 at 3:34pm

German   Offline
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Posts: 118
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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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Reply #3 - Jan 23rd, 2015 at 11:57am

German   Offline
Full Member

Posts: 118
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Hello, Pon. If you are still interested we have resolved the issue. These options have been renamed into new ones. The changes are available in the current UGENE version: http://ugene.unipro.ru/download.html
 
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