BLAT
Description
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Analyzing vertebrate genomes requires rapid mRNA/DNA and cross-species protein
alignments. BLAT (the BLAST-Like Alignment Tool) is a software program developed
by Jim Kent at UCSC to identify similarities between DNA sequences and protein
sequences. It was developed to assist in the annotation of the human genome
sequence. BLAT is much faster than older tools such as BLAST for nucleotide and
protein alignments, and it can also perform spliced alignments of RNA to DNA.
BLAT uses a space-time tradeoff to compare sequences quickly. BLAT precomputes
an index of all nonoverlapping k-mers in the genome. This index fits inside the
RAM of inexpensive computers, and need only be computed once for each genome
assembly. BLAT has several major stages. It uses the index to find regions in
the genome likely to be similar to the query sequence. It performs an alignment
between homologous regions. It stitches together these aligned regions (often
exons) into larger alignments (typically genes). Finally, BLAT revisits small
internal exons possibly missed at the first stage and adjusts large gap
boundaries that have canonical splice sites where feasible.
Template:App Location
Available versions
- 34
Running the application using modules
To use blat with the environment modules system at HPC the following commands are available:
Get module information for blat:
$module spider blat
Load the default application module:
$module load blat
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_BLAT_DIR - directory where blat is located.
- HPC_BLAT_BIN - executable directory
- HPC_BLAT_DOC - documentation directory