Hello, How exactly to do the analysis is a scientific question, but I can help you gain access to the tools:
1) Use the Table browser to download the 3' end of each transcripts that you are interested in. 2) Download and install BLAT to do the comparisions General idea would be to run BLAT with both the query and target being the file from #1, to eliminate self-hits, and to analyze results. Some links: http://genome.ucsc.edu/FAQ/FAQblat http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html We hope this helps, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Hui Liu" <[email protected]> wrote: > From: "Hui Liu" <[email protected]> > To: "genome" <[email protected]> > Sent: Thursday, August 20, 2009 1:38:30 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] alignment among human 3'UTR > > Dear UCSC > How can I carry out a similarity search among the human 3’URT, that > is, for the 3’UTR of each human gene, I want to get similarity scores > between the 3’UTR of this gene and the 3’UTR of all other human genes. > > Thanks > > Hui Liu > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
