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