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