Bioinformatcs Tools for RNAs

Bioinformatics tools for RNAs and their supplementary data

MXSCARNA — by Yasuo Tabei — last modified 2007-05-16 23:50

MXSCARNA (Multiplex Stem Candidate Aligner for RNAs) is a multiple alignment tool for RNA sequences using progressive alignment based on pairwise structural alignment algorithm of SCARNA. This software is fast enough for large scale analyses, while the accuracies of the alignments are better than or comparable with the existing algorithms which are computationally much more expensive in time and memory.

Murlet — by Mituyama Toutai — last modified 2007-05-22 23:30

Murlet is a practical alignment tool for structural RNA sequences. It is based on the Sankoff algorithm and uses an efficient scoring system that considerably reduces the time and space requirements without degrading alignment quality.

RNAmine — by Mituyama Toutai — last modified 2008-03-21 20:39

RNAmine is a software tool to extract the structural motifs from a set of RNA sequences using a graph mining technique. Developed by Mizuho Information & Research Institute.

SCARNA — by Mituyama Toutai — last modified 2008-03-30 08:40

SCARNA is an alignment tool for a pair of RNA sequences based on the predicted common secondary structure.

PHMMTS — by Mituyama Toutai — last modified 2008-03-22 22:26

PHMMTS (Pair Hidden Markov Models on Tree Structures) aligns a sequence of unknown secondary structure to a sequence of known secondary structure.

PSTAG — by Mituyama Toutai — last modified 2008-03-22 22:12

PSTAG (Pair Stochastic Tree Adjoining Grammars) for RNA sequences including pseudoknotted structures.

Rfold — by Kiryu Hisanori — last modified 2007-07-10 21:13

Rfold computes local base pairing probabilities for long DNA sequences.

Stem Kernels — by Kengo Sato — last modified 2008-01-17 19:45

The stem kernel is a kernel function for structural RNAs to measure a kind of similarity between a pair of RNA sequences from the viewpoint of secondary structures.

download — by Asai Kiyoshi — last modified 2008-02-02 07:01

Download page of software.ncrna.org

CentroidFold — by Kengo Sato — last modified 2008-10-04 04:11

CentroidFold based on a generalized centroid estimator is one of the most accurate tools for predicting RNA secondary structures. See the original paper for the details of the algorithm.

miRRim — by Terai Goro — last modified 2008-04-02 21:09

miRRim is a method for detecting miRNA foldbacks based on hidden Markov model (HMM). In this method, the evolutionary and secondary structural features of a miRNA region is represented by a sequence of multidimensional vectors. HMMs that generate a sequence of continuous values are used to model the feature vector sequences.