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Sequence Searcher: A Java tool to perform regular expression and fuzzy searches of multiple DNA and protein sequences
Francesco Marass1, Chris Upton
1Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada. fmarass@uvic.ca
BMC Research Notes
|February 3, 2009
Summary
SeqS is a new bioinformatics tool for searching DNA and protein sequences. It offers platform independence, handles large datasets, and supports both exact and fuzzy pattern matching for efficient sequence analysis.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Existing sequence-searching tools often have limitations such as platform specificity, restrictive size limits, and single-mode search capabilities (DNA or protein only).
- These limitations hinder efficient and flexible sequence analysis in biological research.
Purpose of the Study:
- To develop a user-friendly, fast, and platform-independent tool for searching biological sequences.
- To enable searching for patterns in both amino acid and nucleotide sequences, accommodating single or multiple sequences.
Main Methods:
- Implementation of a novel sequence searching algorithm supporting regular expressions and fuzzy searching.
- Development of a graphical interface for visualizing mismatch positions in fuzzy searches.
- Ensuring platform independence for broad accessibility.
Main Results:
- The developed tool, SeqS, allows for efficient pattern searching across diverse sequence types (protein and nucleic acid).
- It supports both exact (regular expression) and approximate (fuzzy) matching with adjustable error tolerance.
- Fuzzy search results include graphical display of mismatch locations for enhanced interpretation.
Conclusions:
- SeqS offers an advanced feature set compared to existing tools, enhancing sequence analysis capabilities.
- The tool can be utilized as a stand-alone application or integrated into larger bioinformatics workflows and platforms.
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