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  1. UGENE
  2. UGENE-3503

Incorrect "Max hits" option of local BLAST

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    • Tests Type:
      Untestable
    • Sprint:
      DEV-16/10/2014, DEV-06/11/2014, DEV-13/11/2014
    • Affect Type:
      Userdefined

      Description

      Remote BLAST has the option HITLIST_SIZE: http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node37.html
      It is the limit of results count. And this option is called "Max hits" in UGENE.

      HITLIST_SIZE is only the remote BLAST option:

      Irrelevant to wwwblast and standalone commandline BLAST.

      UGENE tries to emulate this option for local BLAST with other ones.
      BLASTALL:

      -K Number of best hits from a region to keep. Off by default.
      If used a value of 100 is recommended. Very high values of -v or -b is also suggested [Integer]

      BLAST+:

      -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

      But it is still called "Max hits". I think that it is wrong because 3 different options are called equally.

      Consider two solutions and choose one of them:
      1) Rename the options for BLASTALL and BLAST+.
      2) Leave this name "Max hits" for the option but implement it with another way: take only first "Max hits" results and throw away other results. This solution could be wrong, investigate it.

      Don't forget to synchronize the changes with the corresponding Workflow Designer elements.

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              Assignee:
              ggrekhov German Grekhov
              Reporter:
              ggrekhov German Grekhov
              Assigned Tester:
              Aleksey Tiunov [X] (Inactive)
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              1 Start watching this issue

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