Motif Finder

Motif finders are tools to find the most conserved secondary structure patters in a set of un-aligned nucleic acids sequences.

MEMERIS — by Mituyama Toutai — last modified 2008-10-27 23:10

MEMERIS is an extension of the MEME (http://meme.nbcr.net/meme/intro.html) motif finder. MEMERIS integrates information about RNA secondary structures into the motif search to guide the search towards single-stranded regions.

RNAMST — by Mituyama Toutai — last modified 2008-10-27 23:34

RNAMST is an efficient and flexible RNA Motif Search Tool for RNA structural homologs.

CMfinder — by admin — last modified 2006-10-27 22:25

CMfinder is a new tool to predict RNA motifs in unaligned sequences. It is an expectation maximization algorithm using covariance models for motif description, featuring novel integration of multiple techniques for effective search of motif space, and a Bayesian framework that blends mutual information-based and folding energy-based approaches to predict structure in a principled way

comRNA — by admin — last modified 2006-10-27 22:25

comRNA enumerates common secondary structural motifs shared in a set of unaligned RNA sequences by using graph mining algorithm.

RNABOB — by admin — last modified 2006-10-27 22:25

RNABOB is an implementation of D. Gautheret's RNAMOT, but with a different underlying algorithm using a nondeterministic finite state machine with node rewriting rules. (Computer scientists would probably cringe in horror. It works, and it's fast, but is it street legal in a computer science department? Who knows.) If you're looking for an RNA motif that fits a hard consensus pattern -- a la PROSITE patterns, but with base-pairing -- you might check out RNABOB.

RNAMOT — by admin — last modified 2006-10-27 22:25

The RNAMOT program finds primary or secondary structure motifs in nucleic acid sequences. RNAMOT inputs consist in a sequence file containing the RNA or DNA sequence(s) to be analyzed and a descriptor file defining the structural motif to be searched. The algorithm and potential applications of RNAMOT have been discussed in detail by Gautheret et al. (CABIOS, 6, 325, 1993).

ERPIN — by admin — last modified 2006-10-27 22:25

ERPIN (Easy RNA Profile IdentificatioN) is an RNA motif search program developped by Daniel Gautheret and André Lambert. Unlike most RNA pattern matching programs, ERPIN does not require users to write complex descriptors before starting a search. Instead ERPIN reads a sequence alignement and secondary structure, and automatically infers a statistical "secondary structure profile" (SSP). An original Dynamic Programming algorithm then matches this SSP onto any target database, finding solutions and their associated scores. In the latest version (unpublished) Erpin computes E-values for matches.