Also, with BLAT tiles that are over-used and are masked out producing no hits. This is to prevent the speed from dropping horrendously on very over-used tiles. Since the example sequence >> AAATGGAAAAGAAAATGAAA is very heavy with A's, this could explain it.
You might try either BWA or bowtie for searching very short sequences. -Galt Jennifer Jackson wrote: > Hello Melissa, > > It is very likely that your sequence is simply too short (20 bases) to > find a match. If possible, try bounding the region with additional > sequence in order to find a BLAT match. > > I tried using the zoom out 1.5x button on the main browser page for hg18 > (top of page) starting with your region chr21:46881236-46881255, > extracted the DNA (DNA link top blue bar) for the new region > chr21:46,881,231-46,881,260, and ran a web BLAT with this sequence > (below, 30 bases). It was enough extra sequence to find two 100% > identity matches. One covered the full 30 bases (chr21 - original > location), the other a 21 base fragment (chr13 - alternate location). > > 30 base query used vs hg18, web BLAT > chr21:46,881,231-46,881,260 > >AGTAGAAATGGAAAAGAAAATGAAATAAAT > > Please try this and see if you can duplicate. > > The types of sequences BLAT will find matches for is defined on this > BLAT page (scroll down): http://genome.ucsc.edu/cgi-bin/hgBlat > > Specifically: > > BLAT on DNA is designed to quickly find sequences of 95% and greater > similarity of length 25 bases or more. It may miss more divergent or > shorter sequence alignments. It will find perfect sequence matches of 25 > bases, and sometimes find them down to 20 bases. BLAT on proteins finds > sequences of 80% and greater similarity of length 20 amino acids or > more. In practice DNA BLAT works well on primates, and protein blat on > land vertebrates. > > Hopefully this helps to explain how BLAT functions, > Jennifer > > --------------------------------- > Jennifer Jackson > UCSC Genome Informatics Group > http://genome.ucsc.edu/ > > On 5/21/10 4:57 PM, Melissa Cline wrote: >> Hi folks, >> >> I'm observing strange behavior, with exactly these steps as follows: >> 1. Go into the round robin browser for hg18 and go to the coordinates >> chr21:46,881,236-46,881,255 >> 2. Extract a copy-able version of the reference genome sequence at >> these coordinates by clicking on the DNA link. That yields this: >>> hg18_dna range=chr21:46881236-46881255 5'pad=0 3'pad=0 strand=+ >>> repeatMasking=none >> AAATGGAAAAGAAAATGAAA >> 3. Go to BLAT, select hg18, enter this sequence in the search window, >> and click Submit. >> >> This yields the message: >> >> Sorry, no matches found >> >> Why can't it find this sequence? What am I missing? >> >> Thanks! >> >> Melissa >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
