RNAPattMatch – a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps

Searching for RNA sequence-structure patterns is becoming an essential tool for RNA practitioners. Novel discoveries of regulatory non-coding RNAs in targeted organisms and the motivation to find them across a wide range of organisms have prompted the use of computational RNA pattern matching as an enhancement to sequence similarity. State-of-the-art programs differ by the flexibility of patterns allowed as queries and by their simplicity of use. In particular-no existing method is available as a user-friendly web server. A general program that searches for RNA sequence-structure patterns is RNA Structator. However, it is not available as a web server and does not provide the option to allow flexible gap pattern representation with an upper bound of the gap length being specified at any position in the sequence.

Here, scientists at Ben-Gurion University introduce RNAPattMatch, a web-based application that is user friendly and makes sequence/structure RNA queries accessible to practitioners of various background and proficiency. It also extends RNA Structator and allows a more flexible variable gaps representation, in addition to analysis of results using energy minimization methods.

rna-seqThe predicted secondary structure of the first found match using Mfold for the secondary structure drawing, while comparing it with the secondary structure drawing of the match itself.

Availability – RNAPattMatch service is available at http://www.cs.bgu.ac.il/rnapattmatch. A standalone version of the search tool is also available to download at the site.

Drory Retwitzer M, Polishchuk M, Churkin E, Kifer I, Yakhini Z, Barash D. (2015) RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps. Nucleic Acids Res [Epub ahead of print]. [article]

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