Using BLAT to Find Sequence Similarity in Closely Related Genomes

Medha Bhagwat1, Lynn Young1, Rex R. Robison1

1 National Institutes of Health Library, National Institutes of Health, Bethesda, Maryland
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 10.8
DOI:  10.1002/0471250953.bi1008s37
Online Posting Date:  March, 2012
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Abstract

The BLAST‐Like Alignment Tool (BLAT) is used to find genomic sequences that match a protein or DNA sequence submitted by the user. BLAT is typically used for searching similar sequences within the same or closely related species. It was developed to align millions of expressed sequence tags and mouse whole‐genome random reads to the human genome at a higher speed. It is freely available either on the Web or as a downloadable stand‐alone program. BLAT search results provide a link for visualization in the University of California, Santa Cruz (UCSC) Genome Browser, where associated biological information may be obtained. Three example protocols are given: using an mRNA sequence to identify the exon‐intron locations and associated gene in the genomic sequence of the same species, using a protein sequence to identify the coding regions in a genomic sequence and to search for gene family members in the same species, and using a protein sequence to find homologs in another species. Curr. Protoc. Bioinform. 37:10.8.1‐10.8.24. © 2012 by John Wiley & Sons, Inc.

Keywords: sequence similarity; alignment; homology; BLAT; UCSC Genome Browser

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Finding the Exon‐Intron Structure of a Gene
  • Basic Protocol 2: Mapping a Protein Sequence to the Genome
  • Support Protocol 1: Viewing All BLAT Matches on the Same Chromosome Simultaneously in the UCSC Genome Browser
  • Basic Protocol 3: Finding a Gene Homolog in the Genome of Another Organism
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

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Figures

Videos

Literature Cited

   Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403‐410.
   Bina, M. 2006. Identification and mapping of paralogous genes on a known genomic DNA sequence. In Methods in Molecular Biology, Vol. 338: Gene Mapping, Discovery, and Expression (M. Bina, ed.) pp. 21‐29. Humana Press, Totowa, N.J.
   Harper, C., Huang, C., Stryke, D., Kawamoto, M., Ferrin, T., and Babbitt, P. 2006. Comparison of methods for genomic localization of gene trap sequences. BMC Genomics 7:236.
   Kent, W.J. 2002. BLAT: The BLAST‐like alignment tool. Genome Res. 12:656–664.
   Morgulis, A., Coulouris, G., Raytselis, Y., Madden, T. L., Agarwala, R., and Schäffer, A.A. 2008. Database indexing for production MegaBLAST searches. Bioinformatics 24:1757–1764.
   Yavatkar, A., Lin, Y., Ross, J., Fann, Y., Brody, T., and Odenwald, W. 2008. Rapid detection and curation of conserved DNA via enhanced‐BLAT and EvoPrinterHD analysis. BMC Genomics 9:106.
Key Reference
   Kent, W.J. 2002. See above.
  The original article by the author of BLAT discusses the rationale and algorithms used in its development.
Internet Resources
   http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BLATAlign
  UCSC online documentation for BLAT.
   http://genome.ucsc.edu/goldenPath/help/blatSpec.html
  BLAT program specifications and user guide.
   http://genome.ucsc.edu/FAQ/FAQblat.html
  FAQ about BLAT.
   http://www.genome.gov/EdKit/pdfs/glossary_final‐linked.pdf
  A glossary of useful terms for understanding genomic research.
   http://blast.ncbi.nlm.nih.gov/Blast.cgi
  BLAST Web site.
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Supplementary Material