It looks like there are some repetitive tiles in your sequence that make it harder to detect.
If you add -repMatch=2048 to standalone blat commandline, you will get the hit you wanted. You could increase it even more and find other lower-quality alignments. I took the default repMatch of 1024 and doubled it because you are using stepSize=5. -Galt On Thu, 12 Mar 2009, Amol Carl Shetty wrote: > Hello > > I have been using the standalone Blat extensively over the last few > months using the following command : > > blat -stepSize=5 -minScore=0 -minIdentity=0 database.2bit query.fa > output.psl > > which replicates the web-based version of the same as specified on the > website (http://genome.ucsc.edu/FAQ/FAQblat). > > > However, I have run into an issue where there is a significant > difference in the results. For example, > > On using the web-based Blat based on the following : > > Genome : Mouse > Assembly : July 2007 > Query Type : DNA > Sequence : > ATTTGTGTGTGTGTGTGTGTTTTTTTTTTTGTTGTTGTTGTTGTTGTTGTTTTGAGACAGGGTTT > > The result obtained is > QUERY SCORE START END QSIZE IDENTITY > CHRO STRAND START END SPAN > --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > YourSeq 65 1 65 > 65 > 100.0% 16 + 62887839 62887903 > 65 > > > However, on using the standalone blast, the same sequence yields no > results. > > Kindly, let me know where the problem lies? > > Thank you > > Amol Carl Shetty > Department of Human Genetics > Emory University > Atlanta, Georgia > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
