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Using BLAT to find sequence similarity in closely related genomes
Medha Bhagwat1, Lynn Young1, Rex R Robison1
1National Institutes of Health Library, National Institutes of Health, Bethesda, Maryland.
Current Protocols in Bioinformatics
|March 6, 2012
Summary
The BLAST-Like Alignment Tool (BLAT) rapidly aligns user-submitted DNA or protein sequences to genomic databases. This tool aids in identifying gene structures, coding regions, and homologous genes across species.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- The BLAST-Like Alignment Tool (BLAT) is a widely used bioinformatics tool.
- It facilitates the identification of homologous sequences within genomic databases.
- BLAT was developed for high-speed alignment of large datasets like expressed sequence tags.
Purpose of the Study:
- To describe the functionality and applications of the BLAST-Like Alignment Tool (BLAT).
- To provide practical examples of using BLAT for sequence alignment and gene identification.
- To highlight BLAT's utility in comparative genomics and gene family analysis.
Main Methods:
- Utilizing BLAT to align submitted DNA or protein sequences against genomic databases.
- Employing BLAT for high-throughput sequence alignment, including expressed sequence tags and genomic reads.
- Leveraging the UCSC Genome Browser for visualization and retrieval of associated biological data.
Main Results:
- BLAT enables rapid identification of sequence similarities within and across species.
- The tool effectively maps mRNA sequences to identify exon-intron structures and associated genes.
- Protein sequence analysis with BLAT reveals coding regions and facilitates homologous gene searches.
Conclusions:
- BLAT is a versatile and efficient tool for genomic sequence analysis.
- Its applications range from gene structure determination to cross-species homology searches.
- BLAT, integrated with the UCSC Genome Browser, provides a powerful platform for biological data exploration.
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