BLAT--the BLAST-like alignment tool.

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. This paper describes how BLAT was optimized. Effects on speed and sensitivity are explored for various K-mer sizes, mismatch schemes, and number of required index matches. BLAT is compared with other alignment programs on various test sets and then used in several genome-wide applications. http://genome.ucsc.edu hosts a web-based BLAT server for the human genome.

[1]  M S Waterman,et al.  Identification of common molecular subsequences. , 1981, Journal of molecular biology.

[2]  D. Lipman,et al.  Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[3]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[4]  O. Gotoh,et al.  Optimal sequence alignment allowing for long gaps. , 1990, Bulletin of mathematical biology.

[5]  Kun-Mao Chao,et al.  Aligning two sequences within a specified diagonal band , 1992, Comput. Appl. Biosci..

[6]  David J. States,et al.  Identification of protein coding regions by database similarity search , 1993, Nature Genetics.

[7]  David J. States,et al.  QGB: Combined Use of Sequence Similarity and Codon Bias for Coding Region Identification , 1994, J. Comput. Biol..

[8]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[9]  Richard Mott,et al.  EST_GENOME: a program to align spliced DNA sequences to unspliced genomic DNA , 1997, Comput. Appl. Biosci..

[10]  M. Boguski,et al.  Evolutionary parameters of the transcribed mammalian genome: an analysis of 2,820 orthologous rodent and human sequences. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[11]  G. Rubin,et al.  A computer program for aligning a cDNA sequence with a genomic DNA sequence. , 1998, Genome research.

[12]  Richard Hughey,et al.  Hidden Markov models for detecting remote protein homologies , 1998, Bioinform..

[13]  Melanie E. Goward,et al.  The DNA sequence of human chromosome 22 , 1999, Nature.

[14]  W. James Kent,et al.  The Intronerator: exploring introns and alternative splicing in Caenorhabditis elegans , 2000, Nucleic Acids Res..

[15]  Lukas Wagner,et al.  A Greedy Algorithm for Aligning DNA Sequences , 2000, J. Comput. Biol..

[16]  Help in accessing human genome information. The International Human Genome Sequencing Consortium. , 2000, Science.

[17]  C. Fizames,et al.  Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence , 2000, Nature Genetics.

[18]  Y Sakaki,et al.  The DNA sequence of human chromosome 21. , 2000, Nature.

[19]  Osamu Gotoh,et al.  Homology-based gene structure prediction: simplified matching algorithm using a translated codon (tron) and improved accuracy by allowing for long gaps , 2000, Bioinform..

[20]  M. Hattori,et al.  The DNA sequence of human chromosome 21 , 2000, Nature.

[21]  International Human Genome Sequencing Consortium.  Initial sequencing and analysis of the human genome , 2001, Nature.

[22]  R. Guigó,et al.  SGP-1: prediction and validation of homologous genes based on sequence alignments. , 2001, Genome research.

[23]  J. Mullikin,et al.  SSAHA: a fast search method for large DNA databases. , 2001, Genome research.

[24]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.