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
