Hi Stefanie, If you click on the column name in the Gene Sorter, you will see the settings that were used in generating the column here:
Method All known splice variants of all known human genes are put into a blast protein database using the formatdb program. This database is then searched with each known gene using version 2.2.5 of the NCBI blastall program with the following flags: -p blastp -e 0.01 -m 8 -b 1000 . . . does this explain the differences you are seeing? If not, please feel free to write back to us at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 12/06/10 09:18, Stefanie Gerstberger wrote: > Hi, > I was checking for one protein the blastp value from the gene sorter compared > to > when I do it manually for the canonical gene ( sequence as given on ucsc) on > ncbi and I noticed that for SMAD5 protein and SMAD2 protein the given score > on > ncbi for their homology is 7e(-153) whereas on the gene sorter e^(-134) or > e^(-135) (depending on which is query and which is subject). How can I > explain > the differences in scores and how can I reproduce the result on ucsc gene > sorter? > Thanks, > Stefanie > > > > --------------------------------------------------- > Stefanie Gerstberger > graduate student in Chemical Biology > Tri-Institutional Program > Cornell University, > Rockefeller University, > Memorial Sloan Kettering Cancer Center > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
