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Finding protein and nucleotide similarities with FASTA
1University of Virginia School of Medicine, Charlottesville, Virginia, USA.
Current Protocols in Bioinformatics
|April 23, 2008
Summary
The FASTA package offers advanced sequence similarity searching for proteins and DNA, providing accurate statistical estimates and enhanced sensitivity for DNA comparisons compared to BLASTN.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Sequence similarity searching is crucial for understanding protein and DNA function.
- Existing tools like BLAST have limitations, especially for short sequences.
- The FASTA package aims to address these limitations with enhanced capabilities.
Purpose of the Study:
- To introduce and detail the FASTA package for sequence similarity searching.
- To highlight FASTA's advantages over BLAST, particularly for short peptides and oligonucleotides.
- To provide protocols for utilizing FASTA in various sequence comparison scenarios.
Main Methods:
- Utilizing the FASTA suite of programs for sequence similarity searches.
- Employing diverse database formats, including MySQL sequence databases.
- Performing protein:protein, protein:DNA, and DNA:DNA comparisons.
Main Results:
- FASTA offers a comprehensive set of similarity searching programs.
- FASTA demonstrates higher sensitivity than BLASTN for DNA sequence comparisons.
- FASTA provides accurate statistical significance estimates for search results.
Conclusions:
- The FASTA package is a powerful and sensitive tool for characterizing protein and DNA sequences.
- FASTA complements existing tools by offering specialized functions for short sequences.
- FASTA's accurate statistical estimates enhance the reliability of sequence similarity analyses.
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