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
