Hello, In summery, our scientists recommend that you first try using the Blat score as an alignment metric. The score covers the entire alignment, not just individual exons.
If that does not meet your needs, then re-running as: "blat -out=blast8" will provide separate exons with blast statistics including the e-value (with a hardwired constant genome size of 3 billion, which should basically be right for most mammals). Complete Blat documentation is either on or linked from here: http://genome.ucsc.edu/FAQ/FAQblat.html Thank you, Jennifer Jackson UCSC Genome Bioinformatics Group Mittal, Vinay K wrote: > Hi, > > I have been using BLAT for my sequence analysis. I was wondering if there is > anyway to find the significance of a particular alignment found by BLAT (like > BLAST has e-value)? > If we run BLAT and set output mode as blast then it will automatically > calculcate e-value but I have aligned my all my sequences with output format > as psl. Is there anyway to calculate e-value from BLAT psl output?? > > Thanks for your help. > > Sincerely, > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
