Hi, Amit! from blat help page: -prot Synonymous with -t=prot -q=prot
I am guessing from the name that the query RefSeqAA.fa is protein. What is the Human2.5Updated.fa ? Is it protein too? -Galt On Fri, 14 Nov 2008, Amit Indap wrote: > Hi UCSC, > > I was wondering about why blat lists negative values for the tStart/End in > this psl result. > > I was aligning an amino acid sequence against PDB records: > > 103 0 0 0 0 0 0 0 + > NP_005347.3 509 123 226 1BHH 108 -152 -49 1 > 103, 123, -152, > > The command I ran was: > > blat Human2.5Updated.fa RefSeqAA.fa -prot -out=pslx -minIdentity=100 > blat100output.pslx > > Have you seen this before? I'm a bit confused, so any help would be great. > > Thanks! > > Amit > > Amit R. Indap > [EMAIL PROTECTED] > > > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
