>I ran blat against this portion of chr1. >This worked fine and turned up 32 hits including >the one that you were expecting. How did you do this in blat? It is difficult to index the entire genome to its full depth when some times would be hit millions of times. Handling repeats exhaustively is not one of BLAT's goals.
Jim Kent is working on a new short-sequence aligner program that might help here, but it is still in development. Repeat RepeatMasker Information Name: L1PA7 Family: L1 Class: LINE SW Score: 16289 Divergence: 8.7% Deletions: 0.8% Insertions: 0.8% Begin in repeat: 3132 End in repeat: 4244 Left in repeat: 1902 Position: chr1:247183181-247184298 Band: 1q44 Genomic Size: 1118 Strand: - -Galt On Tue, 4 Nov 2008, Yuan Jian wrote: > Hi there, > > I got a seuquence > TGAAAACTGGCACAAGACAAGGATGCC > located in chr1:247183338-247183364 strand-. > > but when I blat it. I can not find that location for the sequence. > but I found it in other loci of chr1 and strand-: > browser details YourSeq 27 1 27 27 100.0% 1 - 219139486 219139512 27 > browser details YourSeq 27 1 27 27 100.0% 1 - 192113590 192113616 27 > browser details YourSeq 27 1 27 27 100.0% 1 - 189295101 189295127 27 > browser details YourSeq 27 1 27 27 100.0% 1 - 156553131 156553157 27 > browser details YourSeq 27 1 27 27 100.0% 1 - 156665481 156665507 27 > > > can you please tell me why? > > thanks > > Yu > > > > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
