> Peng Yu wrote: > > I don't find the word 'tile' in BLAT paper. This piqued my interest so I took a look at the paper... instead of "tile", it is referred to as a K-mer, e.g. this spot in the methods section:
K: The K-mer size. Typically this is 8–16 for nucleotide comparisons and 3–7 for amino acid comparisons. There are small mentions of the default settings, "4-mer" and "11-mer". Angie ----- "Galt Barber" <[email protected]> wrote: > From: "Galt Barber" <[email protected]> > To: "Peng Yu" <[email protected]> > Cc: [email protected] > Sent: Monday, April 19, 2010 4:52:56 PM GMT -08:00 US/Canada Pacific > Subject: Re: [Genome] What does tile mean for BLAT? > > A tile is a contiguous set of nucleotides (or amino-acids with > translated blat). The default DNA tileSize is 11 which means > that 11 nucleotides in a row are read and used as a key, > either to store or read information. > > When indexing a DNA target genome database, > BLAT reads the first tile from position 0, > then steps stepSize bases along and reads > the next tile (index-key) at position 11. > This continues with 22, 33, etc. > The default stepSize is set to tileSize. > So the default is non-overlapping tiles. > > But for extra sensitivity with short primer probes we set stepSize to 5. > So in that case the tiles actually overlap. > In that case you are taking a key of size 11 nucleotides > from each position: 0, 5, 10, 15, 20, 25, etc. > > BLAT does not use "spaced-seeds". > > Similarly, when processing the query, > BLAT turns it into tiles and positions, > but for the query the stepSize is always 1. > For each tile of the query, > blat does a lookup in the target database index. > > And then for most uses, the query > is reverse-complemented and the process > repeats. > > -Galt > > Peng Yu wrote: > > I don't find the word 'tile' in BLAT paper. Could you let me know what > > does 'tile' refer to in BLAT? What does 'step' mean in stepSize? > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
