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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.

Sequence Searcher: A Java tool to perform regular expression and fuzzy searches of multiple DNA and protein sequences