Hello UCSC Genome Browser stuff! My name is Guillermo and I downloaded the aligment data of the cDNAs and EST over mm9 genome from Table Browser and now I'm comparing these with my gmap alignment results of the same cDNAs and EST.
I writing to you because I'm not clear about the BLAT alignments filter parameters you used to generate the alignments. The BLAT program specification says "Blat produces .... at the DNA level between two sequences that are of 95% or greater identity ..." ( https://cgwb.nci.nih.gov/goldenPath/help/blatSpec.html). But in addition you may configured the pslReps filter options to only get the alignments over certain amount of coverage (-minCover flag). Did you? I Found some cDNAs cases like BC096042 that at the Table Browser alignments results only have one alignment, but when I put the BC096042 sequence into web version BLAT of the Genome Browser, it shows many alignments, which is expected because there are unfiltered alignments. But what make no sense to me, is that show me many alignment with identity over 95%. Why this alignments aren't at Table Browser? Maybe because in this particular case the BC096042 alignment has a 100% identity and automatically the others sub-optimals alignments were deleted, Is that right? (see the 100% identity alignment also at Genome Browser http://genome.ucsc.edu/cgi-bin/hgc?hgsid=193400045&o=125111868&t=125115317&g=mrna&i=BC096042 ) In order to use your BLAT aligments results from the Table Browser I need to know your filter parameters. Also I would like to confirm the formula (that is used at the hyperlink line) to get the identity from the psl line. I need it to apply to my gmap results and after many attempts, I get to a logical way to calculate it: [(match*100/(match+mismatch+Q gap bases) + match*100/(blocksizes summation)]/2 Please tell me if that's right. Very thanks for your time. I look forward to your reply. -- Guillermo Parada. Undergraduate student Biochemistry at Ponticia Univesidad Católica de Chile. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
