Hello Vera, Use of BLAT for this purpose would not be appropriate.
There are multiple short-sequence aligners available from other sources, although 7 bases is likely past the lower limit for those tools as well. Since you are looking for identical matches, perhaps some simple unix utilities such as "grep" might be the best solution. Or some regular expression functions included in a shell/perl script. We can offer the hg19 genome sequence for download to use locally. To find the versions available, use the path Human -> assembly -> Big Zips or Chromosomes on the Downloads server and then ftp/rsync the data. http://hgdownload.cse.ucsc.edu/downloads.html http://genome.ucsc.edu/FAQ/FAQdownloads.html#download1 http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Download Best wishes for your project, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 5/18/10 8:08 AM, Vera Pendino wrote: > Hi, > I have a very short sequence (7bp) which I would like to find alignments to > the hg19 with any mismatch. > Which are the settings to run BLAT (using gfClient or gfServer ) of short > sequences? > Thank you > Vera > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
