ArticleNucleic acids research2015
RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- Comparative genomics and phylogenomic analyses of lysine riboswitch distributions in bacteria.PloS one · 2017Article
- RNA motif search with data-driven element ordering.BMC bioinformatics · 2016Article
- Nucleic Acid Aptamers: An Emerging Tool for Biotechnology and Biomedical Sensing.Sensors (Basel, Switzerland) · 2015Review
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Authors and funding
6 authors.
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Abstract
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.
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