Fast motif matching in R

Bayesian Markov Model motif discovery tool version 2 - An expectation maximization algorithm for the de novo discovery of enriched motifs as modelled by higher-order Markov models.

PEnG-motif is an open-source software package for searching statistically overrepresented motifs (position specific weight matrices, PWMs) in a set of DNA sequences.

Finding Network Motifs Using MCMC Sampling

RNAelem is a tool for learning secondary structural motifs from a set of RNA sequences.

The software package SiteGA for de novo motif search in ChIP-seq data

Identifying frequent patterns in graphs

HSEARCH: fast and accurate protein sequence motif search and clustering

C++ Codes for the DNA Sequence Motif Discovery Using Greedy Construction Algorithm Based Techniques

An exhaustive GPU algorithm written in C++ to reveal degenerate oligonucleotide motifs written in the 15-letter IUPAC code