Blat is a useful algorithm in the Bioinformatics world dominated with blast! Its even named Blast Like Alignment Tool.
I was recently fiddling with blat alignment on human data, and realized how fast and easy blat can be. Working on next-gen data, Solexa reads is what I had.
One of the cool things was, use the chromosomes separately, run the individual BLAT, and then stitch back the results.
For setting BLAT parameters, and reading/refreshing about the algorithm, these links are really helpful:
I simply ran BLAT on human chromosomes one by one, of course outputting in the popular blast -m9 format to get a pretty table
$ for i in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y; do blat chr$i.fa reads.fa -out=blast9 blat$i.9; done &
Followed by stitching them together with appropriate sorting. I wanted to have them sorted by read, by bit-score, by alignment-length and by chromosome in that order
$ cat *.9 | grep -v ‘#’ | sort -k 1,1 -k 12,12r -k 4,4r -k 2,2 > reads.blat
This gives me a way to look at the top hits, next-best alignments of reads for various analysis on the next-gen Solexa reads.