UNIT 10.8 Using BLAT to Find Sequence Similarity in Closely Related Genomes

  1. Medha Bhagwat,
  2. Lynn Young,
  3. Rex R. Robison

Published Online: 1 MAR 2012

DOI: 10.1002/0471250953.bi1008s37

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

How to Cite

Bhagwat, M., Young, L. and Robison, R. R. 2012. Using BLAT to Find Sequence Similarity in Closely Related Genomes. Current Protocols in Bioinformatics. 37:10.8:10.8.1–10.8.24.

Author Information

  1. National Institutes of Health Library, National Institutes of Health, Bethesda, Maryland

Publication History

  1. Published Online: 1 MAR 2012
  2. Published Print: MAR 2012


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.


  • sequence similarity;
  • alignment;
  • homology;
  • BLAT;
  • UCSC Genome Browser