Abstract
BackgroundMany 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.FindingsWe 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.ConclusionSeqS provides an improved feature set and functions as a stand-alone tool or could be integrated into other bioinformatics platforms.
Highlights
Many sequence-searching tools have limiting factors for their use
Searching for specific patterns in protein and DNA sequences is a common analysis performed by molecular biologists
Detection of restriction enzyme cleavage sites in DNA sequences was an early use of this pattern matching process
Summary
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. Searching for specific patterns in protein and DNA sequences is a common analysis performed by molecular biologists. Searching through genomic sequences for conserved nucleotide patterns such as transcription factor binding sites is another use for this type of analysis.
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