Hello Litao, Blat will find perfect sequence matches of 25 bases, and sometimes find them down to 20 bases. The best solution would probably be to use a different tool for these short alignments. If you really want to use blat, one of our developers has pointed out that you could try using command line blat to accomplish this. You can find general instructions for using command line blat here:
http://genome.ucsc.edu/FAQ/FAQblat#blat3 You may have problems however, if your peptide spans an intron. In this case if you know you are only looking at coding regions you can take all the peptide sequences and make them into a .2bit file. You can find more information on the .2bit file format here: http://genome.ucsc.edu/FAQ/FAQformat#format7 Then you can blat against that as the target database. You will need to set tileSize and stepSize to low values. -stepSize=1 gives the most sensitivity, but takes much more ram. Hopefully this information was helpful and and is enough to get you started. If you have further questions or require clarification feel free to contact the mailing list at [EMAIL PROTECTED] Regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu litao wrote: > Dr sir > > When I use the BLAT server, I found a question. > If I use it with a small peptide(<20), it often have a error > > for example: > Sequence YourSeq is 12 letters long (min is 20), skipping > > But I must alignments of many small peptide sequences alignments to > genome, can you help me to solve it? > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
