Sequence Searcher: A Java tool to perform regular expression and fuzzy searches of multiple DNA and protein sequences
2009
Sequence Searcher: A Tool for DNA and Protein Searches
publication
Author Information
Author(s): Marass Francesco, Upton Chris
Primary Institution: University of Victoria
Conclusion
SeqS is a versatile tool that can be used as a stand-alone program or easily incorporated into more complex bioinformatics workbenches.
Supporting Evidence
- SeqS can search for user-specified patterns in multiple protein and nucleotide sequences.
- The tool can be integrated into other bioinformatics platforms or used as a stand-alone program.
- Results are displayed in sortable tables and include graphical representations of fuzzy matches.
Takeaway
SeqS helps scientists find specific patterns in DNA and protein sequences quickly and easily, like looking for a word in a big book.
Methodology
SeqS uses a brute-force fuzzy search algorithm and supports both regular expression and fuzzy searches for patterns in sequences.
Limitations
SeqS is limited by the amount of memory dedicated to the Java Virtual Machine and may run out of memory during import of sequences or performing a search.
Digital Object Identifier (DOI)
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