RNA Data Analysis and Research

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Introduction to the RSmatch Software

Download & Installation


Many ribonucleic acids (RNAs) play important roles in gene regulation, including non-coding RNAs and cis elements in mRNAs. Some of their functions are attributable to the structure they adopt, which are also called RNA motifs. Like sequence elements, RNA structure elements can be identified by comparing RNAs containing similar structures. The RSmatch package is designed to provide a light-weight approach to compare RNA structures, thereby uncovering functional structure elements. Compared with other tools for RNA structure comparison, RSmatch is fast, requiring quadratic time determined by the sizes of two given structures. 

RSmatch uses two scoring schemes, i.e. position independent and position dependent schemes. The position independent scheme entails two scoring matrices, one for single-stranded regions and the other for double-stranded regions. This scoring scheme is used in pair-wise comparisons and database searches.  The position dependent scheme, also known as profile, scores individual structure positions and is used by the multiple structure alignment and iterative database search functions. RSmatch provides both global and local alignment options even though the latter is more useful in most cases. In addition, RSmatch can take pattern-based structures as input. Please check the following publication for details:

Liu., J., Wang, J.T., Hu, J., and Tian, B. A method for aligning RNA secondary structures and its application to RNA motif detection. BMC Bioinformatics 2005, 6:89

In the current version (2.0), RSmatch provides the following functions: (1)  Pair-wise comparison & Database search (2)  Multiple structure alignment with an extended mode to compute common structure (NEW) (3)  Iterative database search (NEW)

Also, it provides following utilities: (1) We now give the user the option to perform constrained alignment of RNA structures(NEW). This is done in two ways: (a) Using phylogenetic information to derive the information content at each position of the RNA structure. (b) User-defined specification of conserved region. (2) Slide folding

These functions are described in detail below:

  1. Pair-wise comparison and Database Search (pmatch):

This function finds the RNA structures in the database that locally or globally match a given query structure. This function can also be used to detect motif occurrences in a RNA structure database when the query structure is a known motif with a defined pattern.

  1. Multiple structure alignment with an extended mode to compute common structure (mmatch):

RSmatch constructs a multiple alignment for a given set of RNA structures by progressively expanding the alignment one at a time. This function is useful when a small set of RNAs are functionally related by a shared motif. This function has been enhanced to compute common structure for a group of related RNA sequences.

  1. Iterative database search (imatch):

For iterative database search, RSmatch is able to continuously conduct database searches using a position-specific scoring matrix and update the matrix using the latest result. This function could be much more sensitive than the regular database search, but at the cost of computing time.

Please contact jason.t.wang@njit.edu for comments/suggestions/queries. 

Download & Installation

RADAR/RSmatch fast download version for UNIX and Windows


Then, download the following files and place them in the directory containing the RADAR.jar file:

1) codeTable.properties

2) scoreMat.homo

3) scoreMat.pattern

4) scoreMat.structure

Note: The above files do not depend on Vienna RNA package and hence requires RNA secondary structure input.

Following document provides instructions regarding executing the jar file: