The 3of5 web application for complex and comprehensive pattern matching in protein sequences

Background: The identification of patterns in biological sequences is a key challenge in genome analysis and in proteomics. Frequently such patterns are complex and highly variable, especially in protein sequences. They are frequently described using terms of regular expressions (RegEx) because of the user-friendly terminology. Limitations arise for queries with the increasing complexity of patterns and are accompanied by requirements for enhanced capabilities. This is especially true for patterns containing ambiguous characters and positions and/or length ambiguities. Results: We have implemented the 3of5 web application in order to enable complex pattern matching in protein sequences. 3of5 is named after a special use of its main feature, the novel n-ofm pattern type. This feature allows for an extensive specification of variable patterns where the individual elements may vary in their position, order, and content within a defined stretch of sequence. The number of distinct elements...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Markus Seiler, Alexander Mehrle, Annemarie Poustka, Stefan Wiemann
• Keywords: BMCBI 2006, N-of-m Pattern Type, Pattern Type, Protein Sequences