[Bioclusters] sensitivity & blast

Pamela Culpepper pculpep at hotmail.com
Wed Apr 6 15:23:52 EDT 2005

Lik Mui,

Set the Y value somewhat larger than the product of your two sequence 


>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
>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 
>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

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