WebMOTIFS is an online tool for motif discovery, scoring, analysis, and visualization. It allows you to use different programs to search for DNA-sequence motifs, and to easily combine and evaluate the results.
DEME (Discriminatively Enhanced Motif Elicitation) is a discriminative motif discovery algorithm for use with protein and DNA sequences. Using a probabilistic framework, DEME discovers motifs that are overrepresented in a set of “positive” sequences relative to a “negative” set.
Tmod (Toolbox of Motif Discovery) is developed for the users of Windows operating systems, and has an easy-to-use graphical user interface (GUI). Tmod integrates twelve motif discovery programs: AlignACE (Roth et al., 1998), BioProspector (Liu et al., 2001), Consensus (Hertz and Stormo, 1999), MEME (Bailey and Elkan, 1994), MDscan (Liu et al., 2002), MotifSampler(Thijs, et al., 2001; Thijs, et al., 2002), SeSiMCMC (Favorov, et al., 2005), GLAM (Frith, et al., 2004), MotifRegressor(Conlon, et al., 2003), YMF(Sinha and Tompa, 2003), Weeder (Pavesi, et al., 2001; Pavesi, et al., 2004; Pavesi, et al., 2004) and Gibbs Motif Sampler (Liu, et al., 1995; Newberg, et al., 2007; Thompson, et al., 2004; Thompson, et al., 2003; Thompson, et al., 2007). The motif finding algorithms included in Tmod have all been widely cited and proved excellent methods in the research field of motif discovery.
Hanchang Sun, Yuan Yuan, Yibo Wu, Hui Liu, Jun S. Liu and Hongwei Xie. Tmod: Toolbox of Motif Discovery.
Bioinformatics 2009; doi: 10.1093/bioinformatics/btp681.
MITSU (Motif discovery by ITerative Sampling and Updating) is a command line application for the discovery of transcription factor binding site (TFBS) motifs.
BayesMotif is a de novo identification algorithm for finding a common type of protein sorting motifs in which a highly conserved anchor is present along with a less conserved motif regions.
The BLSSpeller software provides 3 main functionalities to the user: de novo comparative motif discovery, pattern matching (with BLS cutoff) and target prediction.
TEISER (Tool for Eliciting Informative Structural Elements in RNA) is a robust and powerful framework for discovering post-transcriptional regulatory elemenets.
