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]
where database is the name of the database used for the alignment, query is the name of the input file of sequence data in fasta/nib/2bit format, and output_alignment.txt is the output alignment file.

Additional parameters for BLAT alignment can be found in the manual, or by using:

$ blat

Running BLAT on Tusker with query file input_reads.fasta and database db.fa is shown below:

#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 --nodes=1, #SBATCH --ntasks-per-node=1) it is still much faster than the other alignment tools.

BLAT Output

BLAT output is a list containing the following information:

  • the score of the alignment
  • the region of query sequence that matches the database sequence
  • the size of the query sequence
  • the level of identity as a percentage of the alignment
  • the chromosome and position that the query sequence maps to