BLAT is a pairwise alignment tool similar to BLAST. It is more accurate and about 500 times faster than the existing tools for mRNA/DNA alignments and it is about 50 times faster with protein/protein alignments. BLAT accepts short and long query and database sequences as input files.
The basic usage of BLAT is:
$ blat database query output_alignment.txt [options]
fasta/nib/2bitformat, and output_alignment.txt is the output alignment file.
Additional parameters for BLAT alignment can be found in the manual, or by using:
Running BLAT on Crane with query file
input_reads.fasta and database
db.fa is shown below:
#!/bin/sh #SBATCH --job-name=Blat #SBATCH --nodes=1 #SBATCH --ntasks-per-node=1 #SBATCH --time=168:00:00 #SBATCH --mem=50gb #SBATCH --output=Blat.%J.out #SBATCH --error=Blat.%J.err module load blat/35x1 blat db.fa input_reads.fasta output_alignment.txt
Although BLAT is a single threaded program (
#SBATCH --ntasks-per-node=1) it is still much faster than the other alignment tools.
BLAT output is a list containing the following information: