[Bioclusters] sensitivity & blast

Pamela Culpepper pculpep at hotmail.com
Wed Apr 6 16:19:21 EDT 2005


Lik Mui,

We built a test case of the Y value.

The Y value is the database represented as one big sequence.  This, then, 
directly affects the -e, or expectation value.

You are on the right path.

Pam

>From: "Pamela Culpepper" <pculpep at hotmail.com>
>Reply-To: "Clustering,  compute farming & distributed computing in life 
>science informatics" <bioclusters at bioinformatics.org>
>To: bioclusters at bioinformatics.org
>Subject: RE: [Bioclusters] sensitivity & blast
>Date: Wed, 06 Apr 2005 19:23:52 +0000
>
>Lik Mui,
>
>Set the Y value somewhat larger than the product of your two sequence 
>lengths.
>
>Pam
>
>
>
>>From: "L. Mui" <lmui at stanford.edu>
>>Reply-To: "Clustering,  compute farming & distributed computing in life 
>>science informatics" <bioclusters at bioinformatics.org>
>>To: bioclusters at bioinformatics.org
>>CC: lmui at stanford.edu
>>Subject: [Bioclusters] sensitivity & blast
>>Date: Wed,  6 Apr 2005 10:47:19 -0700
>>
>>
>>Hello,
>>
>>We ran into an issue involving blastall, which I suspect folks in this 
>>list
>>might know the answer to.  (I am fairly new to using blastall).  Blastall
>>seems to be sensitive to the input sequence size in detecting HSP. In 
>>other
>>words, depending on length of input, it sometimes does not report all HSP
>>(even with very large -b and -v).
>>
>>We want to standardize blastall across all input sizes.  I am trying out 
>>the
>>following 2 methods, both of which seem to elicit the "right" results:
>>
>>(1) modifying the "-e" e-value threshold by the input size
>>     e.g., if m = input sequence size, run blastall with
>>           "-e 10m"
>>     rationale: the E-value is a function of (mn)
>>
>>(2) fixing the search space (-Y): which seems to fix some statistical
>>parameters for blastall's calculations
>>     e.g., "-Y 168000000000" for a human genome target
>>
>>Could you suggest whether we are on the right track?  What is the right
>>approach to set a uniform sensitivity for all inputs?
>>
>>Many thanks for your help in advance.
>>
>>            Lik Mui
>>_______________________________________________
>>Bioclusters maillist  -  Bioclusters at bioinformatics.org
>>https://bioinformatics.org/mailman/listinfo/bioclusters
>
>
>_______________________________________________
>Bioclusters maillist  -  Bioclusters at bioinformatics.org
>https://bioinformatics.org/mailman/listinfo/bioclusters




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