A Burrows Wheeler Transform -based aligner such as BWA or Bowtie will be able to handle short matches.
Also, you should be aware that on hg19, a 7bp with a mismatch will probably return many thousands of matching locations. The probability of a match at one location is 7/(4^6) = 0.1%. But you have billions of locations you could match at. If your are doing a motif-search, you might want to try one of the specialized motif-search tools available. -Galt Ar 5/18/2010 11:24 AM, scríobh Jennifer Jackson: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
