Sequence Searcher : a Java tool to perform regular expression and fuzzy searches of multiple DNA and protein sequences
Date
2009-01-30
Authors
Marass, Francesco
Upton, Christopher
Journal Title
Journal ISSN
Volume Title
Publisher
BioMed Central
Abstract
Background: Many sequence-searching tools have limiting factors for their use. For example, they
may be platform specific, enforce restrictive size limits and sequences to be searched, or only allow
searches of one of DNA or protein.
Findings: We present an easy-to-use, fast, platform-independent tool to search for amino acid or
nucleotide patterns within one or many protein or nucleic acid sequences. The user can choose to
search for regular expressions or perform a fuzzy search in which a particular number of errors is
accepted during matching of a sequence. Positions of mismatches in fuzzy searches are displayed
graphically the user.
Conclusion: SeqS provides an improved feature set and functions as a stand-alone tool or could
be integrated into other bioinformatics platforms.
Description
BioMed Central
Keywords
Citation
Marass and Upton. Sequence Searcher: a Java tool to perform regular expression and fuzzy searches of multiple DNA and protein sequences. BMC Research Notes 2009, 2:14