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, we 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. 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.
Department of Computer Science, Ben-Gurion University, Beer-Sheva 84105, Israel.
Matan
M
Drory Retwitzer
Department of Computer Science, Ben-Gurion University, Beer-Sheva 84105, Israel Department of Computational Biology, Vavilov Institute of General Genetics, Russian Academy of Science, Moscow 11933, Russia.
Maya
M
Polishchuk
Department of Computer Science, Ben-Gurion University, Beer-Sheva 84105, Israel.
Elena
E
Churkin
Agilent Laboratories, Agilent Technologies, Tel Aviv 49527, Israel Microsoft R&D Center, Herzliya 46725 , Israel.
Ilona
I
Kifer
Agilent Laboratories, Agilent Technologies, Tel Aviv 49527, Israel Laboratory of Computational Biology, Computer Science Department, Israel Institute of Technology, Haifa 32000, Israel.
Zohar
Z
Yakhini
Department of Computer Science, Ben-Gurion University, Beer-Sheva 84105, Israel dbarash@cs.bgu.ac.il.
Danny
D
Barash
D020407:Internet; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D012313:RNA / Q000737:chemistry*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
D012313:RNA