Hello Vera, Yes, this is possible, but you will need to obtain the reference genome sequence, coordinates that you want to mask, do the masking, then run BLAT on your own server against the newly created file.
(using hg19 as an example in links, if using hg18, swap in that database for the links). FTP sequence: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/ Obtain CDS coordinates: Use Table browser or Downloads server, a Gene Prediction track (UCSC Genes, RefSeq Genes, CCDS, etc.), and output or ftp the CDS coordinates. Table browser (good even if using FTP to learn table names/fields. See track descriptions to review methods and select proper dataset for your purposes). http://genome.ucsc.edu/cgi-bin/hgTables http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html Ftp complete files (representing mySQL tables): http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ BLAT: http://genome.ucsc.edu/FAQ/FAQblat.html Hopefully this will help you to get started, please let us know if you need more help, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 6/1/10 8:58 AM, Vera Pendino wrote: > Hi, > I would like to run blat with a short sequence on the regions that are > annotated as intronic, intergenic and UTRs in the human genome(hg19). > In other words, I'd like to know if it is possible to mask the coding regions > of the genome. > Could you help me? > 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
