Hello Jing, The BLAT alignments that are contained in tracks (and generated by the BLAT server) contain statistics that cover the entire match.
If you wanted to capture per-block statistics there are two possibilities (both would require you to do some file manipulation using your own tools): 1) run BLAT locally with alignments in the output, then parse each block's alignment to generate statistics 2) run BLAT locally with just regular PSL output, use those coordinates to break the query sequence up into per-block sections, then run the individual sections of sequence as another BLAT. If you are interested in either of these, this is the BLAT FAQ. Some guidelines for tuning parameters are included in the BLAT Specification document. http://genome.ucsc.edu/FAQ/FAQblat.html Jennifer --------------------------------- Jennifer Jackson UCSC Genome Bioinformatics Group http://genome.ucsc.edu/ On 2/18/10 3:05 PM, Ma, Jing wrote: > Hi, > > Do you have human-mouse alignment results which contain sequence identity > info for each alignment block available for download? > > Thanks, > Jing > > Jing Ma > St. Jude Children's Research Hospital > > ________________________________ > Email Disclaimer: www.stjude.org/emaildisclaimer > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
