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
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