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

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.

Nucleic Acid Aptamers: An Emerging Tool for Biotechnology and Biomedical Sensing

“…Computational algorithms were used to predict the truncated aptamer sequences and secondary structures. For example, Giangrande and co-workers have used a “rational truncation” approach guided by RNA structure prediction and RNA/target docking algorithms to truncate an RNA aptamer to prostate-specific membrane antigen (PSMA), which retains protein binding activity and functionality [ 74 , 75 , 76 , 77 , 78 , 79 , 80 ]. Other techniques such as partial fragmentation were used to determine the minimal binding sequence of DNA aptamers for platelet-derived growth factor (PDGF) protein [ 81 ].…”

Comparative genomics and phylogenomic analyses of lysine riboswitch distributions in bacteria

“…An understanding of the regulatory role of riboswitches along with our ability to manipulate them relies on their accurate identification and on the information about the pattern of riboswitch distribution, the nature of genes they regulate and the latter’s role in metabolism and transport. Several methods [ 15 – 20 ] have been developed for computational detection of riboswitches. Among them, covariance models (CMs) have been the most influential and widely used method of riboswitch detection because it considers both sequence and structural conservation in the aptamer domain [ 21 ].…”

Strict pattern matching under non-overlapping condition

“…Diverse pattern matching methods have been investigated such as string similarity search [12], windowed subsequence matching [13], circular string matching [14], approximate string matching [15], and string searching in large spatial databases [16]. Recently, a new kind of wildcard, named gap constraint (or flexible wildcard [17,18]), is widely used in the tasks of pattern matching [19] and sequential pattern mining [20,21], since it is not only more flexible than traditional wildcards such as "?" and "*", but also more easy to meet users' requirements.…”

“…and "*", but also more easy to meet users' requirements. For instance, pattern matching with gap constraints now is an essential task in searching for RNA sequence-structure pattern [19]. Hence, many researchers have paid increasing attention to handling this kind of challenging issue.…”