On Mon, Apr 19, 2010 at 11:21 PM, Angie Hinrichs <[email protected]> wrote: >> 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".
Just some of my thought. Is it better to make the documentation use the same terminology as the paper to avoid any confusion? > 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 > -- Regards, Peng _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
