Hi Galt, Thanks a lot for your explanation!
Best, Shuli On 11/22/2010 01:59 PM, Galt Barber wrote: > 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
