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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's license makes it free for non-commercial use.1
BLAT is more accurate and much faster than older tools such as BLAST for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences (e.g. BLAST).
BLAT's 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 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.23
See also
- BLAST Basic Local Alignment Search Tool
- Sequence alignment software
References
- ^ Frequently asked questions about BLAT at kentinformatics.com
- ^ Kent, W James (2002). "BLAT--the BLAST-like alignment tool.". Genome research 12 (4): 656–64. doi:. PMID 11932250, http://view.ncbi.nlm.nih.gov/pubmed/11932250. Retrieved on 3 November 2007.
- ^ Hinrichs, A S; D Karolchik, R Baertsch, G P Barber, G Bejerano, H Clawson, M Diekhans, T S Furey, R A Harte, F Hsu, J Hillman-Jackson, R M Kuhn, J S Pedersen, A Pohl, B J Raney, K R Rosenbloom, A Siepel, K E Smith, C W Sugnet, A Sultan-Qurraie, D J Thomas, H Trumbower, R J Weber, M Weirauch, A S Zweig, D Haussler, W J Kent (2006- Jan- 1). "The UCSC Genome Browser Database: update 2006.". Nucleic acids research 34 (Database issue): D590–8. doi:. PMID 16381938, http://view.ncbi.nlm.nih.gov/pubmed/16381938. Retrieved on 3 November 2007.
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