Hello Lise, You may find this help doc on PSL format useful:
http://genome.ucsc.edu/goldenPath/help/customTrack.html#PSL In particular note the minus strand sections. For proteins, the logic described for qStart at the very of this document is applied instead to tStart. Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [email protected]. Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 5/5/11 5:02 AM, lise andrieux wrote: > Good morning, > > Recently I have been using BLAT_V34 (command line) with peptidic queries > against the latest version of human genome (hg19), using the option > "-t=dnax" for translated database and -q=prot for the query > > It works fine with peptides from protein on the plus strand : in the psl > output file (I use the default option) the first figure of the last column, > giving the Tstarts (separated by commas), is matching the number in column > 16, which is the target start Tstart. > > However there's a problem with minus strand peptides: none of the figures of > the last column match numbers in the Tstart or Tend column (16 or 17 ). > > I then did a quick test with dna against dna for a protein on the minus > strand (file test.blat.pb.rna.fa giving result > test.blat.pb.rna_genomehg19.psl), and the same test with the protein > sequence against translated dna(file test.blat.pb.prot.fa giving result > test.blat.pb.prot_genomehg19.psl), ; the first test works, not the second, > thus pointing at a problem with minus strand proteins and blatx (-t=dnax, > -q=prot). > > I also join another file of blatx results with this same problem, starting > at line 302 when the strand is changing from +/+ to +/-. > > Thanks for any help with that problem. > > Best regards, > > > Lise > > Lise Andrieux, PhD > Computational Genomics > Life Sciences DPT > Barcelona Supercomputing Center > Barcelona, Catalunya, > Spain > > ------------------------------------------------------------------------ > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
