Bioinformatics Links Directory : Motifs

Included are RNA motif search programs to help analyze recurrent subsets of nucleotide arrangements in secondary or tertiary structure.

DIAL - (Found July 2, 2008 )

DIAL (dihedral alignment) is a server that provides access to a dynamic programming algorithm for structural alignment of RNA.
http://bioinformatics.bc.edu/clotelab/DIAL/

RNAMST - (Found July 2, 2008 )

RNA Motif Search Tool (RNAMST) is a tool for identifying homologs of a pre-defined RNA structural motif among numerous RNA sequences.
http://bioinfo.csie.ncu.edu.tw/~rnamst/

RNAMOT - (Found July 2, 2008 )

RNA motif search program; not a Web-tool.
http://www.esil.univ-mrs.fr/~dgaut/download/

RNABOB - (Found July 2, 2008 )

Fast RNA motifpattern searcher; from the authors: 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; not a Web-tool; based on RNAMOT.
http://www.genetics.wustl.edu/eddy/software/#rnabob

RNA Analyzer - (Found July 2, 2008 )

RNA Analyzer searches for known structures and identifies RNA motifs in your input sequence.
http://rnaanalyzer.bioapps.biozentrum.uni-wuerzburg.de/

RADAR - (Found July 2, 2008 )

RADAR (RNA Data Analysis and Research) provides multiple tools for RNA structure analysis including: pairwise structure alignment, multiple structure alignment, constrained structure alignment, database searching, and prediction of the consensus structure for a set of RNA sequences.
http://datalab.njit.edu/biodata/rna/RSmatch/server.htm

QuadFinder - (Found July 2, 2008 )

QuadFinder is a tool for the identification and analysis of quadruplex forming nucleotide sequences.
http://miracle.igib.res.in/quadfinder/

QGRS Mapper - (Found July 2, 2008 )

Quadruplex forming G-Rich Sequences (QGRS) Mapper searches nucleotide sequences for the presence of G-quartet motifs. QGRS Mapper allows you to view the distribution and composition of QGRS in the context of alternatively spliced isoforms of your gene.
http://bioinformatics.ramapo.edu/QGRS/index.php

PatSearch - (Found July 2, 2008 )

PatSearch is a pattern matcher that is able to search for specific combinations of oligonucleotide consensus sequences, secondary structure elements and position-weight matrices.
http://bighost.area.ba.cnr.it/BIG/PatSearch/

NDB Tools - (Found July 2, 2008 )

The Nucleic Acid Database (NDB) Tools page includes RNAView and BPView, programs for the visualization and classification of RNA base pairs, motifs, and structures.
http://ndbserver.rutgers.edu/services/