Shalom! Do you know about isPcr ? It's a BLAT-based tool that comes with the BLAT package and it's optimized for primer probe pairs for PCR amplification. http://genome.ucsc.edu/cgi-bin/hgPcr
As far as more sophisticated filtering of blat psl results including coverage, we recommend using pslReps and pslCDnaFilter. Refer to the BLAT FAQ for more info: http://genome.ucsc.edu/FAQ/FAQblat -Galt On Thu, 29 Jan 2009, shlomit farkash wrote: > Hello, > > Sorry, I have another question about using blat for probe design. I have > probes with length ranging from 45 to 60, I am trying to find whether > there are other places in the genome with about 10% mismatch (the most) > besides the 100% match to exclude this probe from my list (it is not > considered unique for hybridization purposes). when using 95% min > identity, I get a hit even with a stretch of 8 mismatches (out of 60), > since it is considered as a single gap ? can I take these gaps into > account as well when searching for a hit? > > Thanks a lot, > Shlomit Amar-Farkash > The Hebrew university, Jerusalem > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
