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Automated Querying of Genome Databases

PLoS Computational Biology

Public Library of Science

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      Confidence Limits on Phylogenies: An Approach Using the Bootstrap

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        BLAT--the BLAST-like alignment tool.

         W. Kent (2002)
        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.
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          EMBOSS: the European Molecular Biology Open Software Suite.

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            Author and article information

            Affiliations
            Whitehead Institute, United States of America
            Author notes
            Peter Schattner is with the Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America. E-mail: schattner@ 123456soe.ucsc.edu
            Contributors
            Role: Editor
            Journal
            PLoS Comput Biol
            pcbi
            PLoS Computational Biology
            Public Library of Science (San Francisco, USA )
            1553-734X
            1553-7358
            January 2007
            26 January 2007
            : 3
            : 1
            1782033
            17257048
            10.1371/journal.pcbi.0030001
            plcb-03-01-04
            (Editor)
            Copyright: © 2007 Peter Schattner. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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            Pages: 6
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            Education
            Custom metadata
            Schattner P (2007) Automated querying of genome databases. PLoS Comput Biol 3(1): e1. doi: 10.1371/journal.pcbi.0030001

            Quantitative & Systems biology

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