Hello Sujata, To extract non-coding alignments, use the Table browser along with Galaxy. Send the Conservation track's MAF output to Galaxy, a custom track of coordinates to Galaxy, then use the tools there to "slice" out regions. See the section Fetch Alignments: http://g2.bx.psu.edu/
Just for your information, to extract coding regions from a MAF alignment, these are the instructions: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#FASTA Using the Table browser alone, you can however extract fasta formatted sequence from any assembly and then run your own BLAT to generate an alignment, tuning the parameters for your specific needs if using command-line BLAT. Start with a track that has defined coding/non-coding regions if you need mRna sequence (Gene and Gene Predictions group - UCSC Genes would be the best choice). Then extract the sequence - either the mRna for the UTR region or the genomic reference sequence that was aligned to. Table browser: http://genome.ucsc.edu/cgi-bin/hgTables Instructions: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#Sequence If you want to use the genomic reference sequence and know the coordinates (do not want to start with a Gene track), use these instructions. Extracting sequence in batch from an assembly: http://genome.ucsc.edu/FAQ/FAQdownloads#download32 Next, run a BLAT using our web server (for smaller projects) or configure your own and run it command-line (any unix platform). BLAT documentation with links to resources: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BLATAlign http://genomewiki.ucsc.edu/index.php/Blat_Scripts Results from BLAT that you run independent of the Browser can be uploaded again as a custom track for more analysis if desired. Custom tracks: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks Command line utilities: http://genomewiki.cse.ucsc.edu/index.php/Kent_source_utilities http://genome.ucsc.edu/FAQ/FAQdownloads#download27 We hope this helps to get you started. If you need more assistance, please email the [email protected] mailing list directly as the team will be working together to answer questions over the next two weeks. Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "sujata roy" <[email protected]> wrote: > From: "sujata roy" <[email protected]> > To: [email protected] > Sent: Friday, December 18, 2009 11:36:43 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] (no subject) > > Dear sir, > Can you please tell me how can I get 3′ UTR alignments for different > species.. > sujata > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
