[Bioperl-l] 2 psi-blast questions

[Donald G. Jackson]

My apologies; I misunderstood the question.

Don Jackson

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 
>>below zero.  
>>    
>>
>
>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" (`<=').
>
>Andreas.
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>  
>