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