Hi, Shuli! The discussion you mention on the FAQ and Wiki was focused on aligning short query sequences.
However, in your case, you are aligning a large mRNA multi-exon sequence which possibly happens to have some tiny exons. In each case the tiny exons, which are too small to independently seed an alignment, will be found to lie somewhat near to a much larger exon. The normal seed extension alignment uses banded dynamic programming and can this find some smaller exons if the score does not drop too much and the tiny exons are not too far away. -Galt On 11/22/10 11:37, Shuli Kang wrote: > Hi there, > > I'm confused by the shortest alignment between query and the genome that > could be found by BLAT. > > 1. According to official BLAT FAQ at > http://genome.ucsc.edu/FAQ/FAQblat.html#blat8: > > /The formula to find the shortest query size that will guarantee a match > (if matching tiles are not marked as overused) is: > 2 * stepSize + tileSize - 1 > For example, with stepSize set to 5 and tileSize set to 11, matches of > query size 2*5+11-1 = 20 bp will be found, if the query matches the > target exactly. The stepSize parameter can range from 1 to tileSize. The > tileSize parameter can range from 6 to 15./ > > 2. According to http://genomewiki.ucsc.edu/index.php/Blat-FAQ > > /This is the smallest size that blat can find an exact match for as you > pointed out: > tileSize + stepSize - 1 = 11 + 5 - 1 = 15/ > > 3. However, according to my own experience, I could found an alignment > of 7 nucleotides by using default BLAT parameters ( > stepSize=tileSize=11). You could see this if you alignment RefSeq > sequence of NM_017954 to HG19. The 7-nt exon has also been included in > the official RefSeq track (chr7:122,120,175-122,120,183) (Unfortunately, > it should be an artificial alignment if you checked the splicing sites > and compared this annotation with Ensemble annotation of ENST00000449022). > > Could anyone give me some explanation? > > Thanks in advance! > Shuli > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
