BLAT (bioinformatics)
Encyclopedia
Analyzing vertebrate
genome
s 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's license makes it free for non-commercial use.
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-mer
s 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 exon
s) into larger alignments (typically gene
s). Finally, BLAT revisits small internal exons possibly missed at the first stage and adjusts large gap boundaries that have canonical splice sites where feasible.
Vertebrate
Vertebrates are animals that are members of the subphylum Vertebrata . Vertebrates are the largest group of chordates, with currently about 58,000 species described. Vertebrates include the jawless fishes, bony fishes, sharks and rays, amphibians, reptiles, mammals, and birds...
genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
s requires rapid mRNA/DNA and cross-species protein alignments
Sequence alignment
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are...
.
BLAT (the BLAST
BLAST
In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...
-Like Alignment Tool) is a software program developed by Jim Kent
Jim Kent
William James Kent is an American research scientist and computer programmer. He has been a contributor to genome database projects and the 2003 winner of the Benjamin Franklin Award .- Early life :...
at UCSC to identify similarities between DNA sequences and protein sequences. It was developed to assist in the annotation of the human genome
Human genome
The human genome is the genome of Homo sapiens, which is stored on 23 chromosome pairs plus the small mitochondrial DNA. 22 of the 23 chromosomes are autosomal chromosome pairs, while the remaining pair is sex-determining...
sequence. BLAT's license makes it free for non-commercial use.
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
Space-time tradeoff
In computer science, a space–time or time–memory tradeoff is a situation where the memory use can be reduced at the cost of slower program execution...
to compare sequences quickly. BLAT precomputes an index of all nonoverlapping k-mer
K-mer
The term k-mer usually refers to a specific n-tuple or n-gram of nucleic acid or amino acid sequences that can be used to identify certain regions within biomolecules like DNA or proteins...
s in the genome. This index fits inside the RAM
Ram
-Animals:*Ram, an uncastrated male sheep*Ram cichlid, a species of freshwater fish endemic to Colombia and Venezuela-Military:*Battering ram*Ramming, a military tactic in which one vehicle runs into another...
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 exon
Exon
An exon is a nucleic acid sequence that is represented in the mature form of an RNA molecule either after portions of a precursor RNA have been removed by cis-splicing or when two or more precursor RNA molecules have been ligated by trans-splicing. The mature RNA molecule can be a messenger RNA...
s) into larger alignments (typically gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
s). Finally, BLAT revisits small internal exons possibly missed at the first stage and adjusts large gap boundaries that have canonical splice sites where feasible.