[Bioperl-l] 2 psi-blast questions
Donald G. Jackson
donald.jackson at bms.com
Fri Jan 30 08:41:38 EST 2004
My apologies; I misunderstood the question.
Andreas Bernauer wrote:
>Donald G. Jackson wrote:
>>Hadas Leonov wrote:
>>>I noticed that a psi-blast report only considers new hits if the 0.0 <
>>>E-value < 0.01 (?).
>>>Is there any possibility to change these parameters ? especially the
>>>0.0 limit, cause large query sequences with 60% identity might still
>>>give an e value of 0.0, thereby causing me to miss them completely by
>>You can set the -h value ($blaster->h()) to adjust the inclusion
>>threshold for refining the scoring matrix. However, it only takes
>>expect values - not identity/length - and the expect value can't go
>I think he meant that evalues that are exactly zero get excluded, as
>the threshold is tested with a "lower than" (`<') instead of an "lower
>or equal than" (`<=').
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