BLAT

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Application data

Created by Jim Kent
Principal bioinformatics method(s) Read mapping, Sequence alignment
Maintained? Maybe
Input format(s) FASTA
Software features Read mapping
Programming language(s) C
Licence Freeware
Operating system(s) Linux, Mac OS X

Summary: Fast, accurate spliced alignment of DNA sequences

Analyzing vertebrate genomes requires rapid mRNA/DNA and cross-species protein alignments. A new tool, BLAT, is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences. BLAT's speed stems from 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 homologous 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.

Links


References

  1. Kent WJ. 2002. Genome Research


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