Hello Tony, Unfortunately BLAT is not designed to work with very short sequences.
You can still use the output of other tools with the UCSC database. Simply convert the files to one of the Custom track data formats and upload to use along with the rest of your target assembly. http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks Thanks, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 5/5/10 6:14 AM, Anthony Dallosso PhD wrote: > Hi > > is it possible to use the BLAT or in silico PCR tool on UCSC to identify > the location of primers/short sequences targeted to bisulphite modified DNA > ? > > Although tools such as methblast and bisearch are functional, it would be > very useful for me to have this capability linked to UCSC, so I can map > hits by genome coordinates for instance. > > bw > > Tony > > > ---------------------- > Anthony R. Dallosso PhD > CLIC Sargent Research Unit > Dept of Cellular& Molecular Medicine > [email protected] > 0117 (33)12043 > http://www.bristol.ac.uk/cancer/research/dallosso.html > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
