motif-x (short for motif extractor) is a software tool designed to extract overrepresented patterns from any sequence data set. The algorithm is an iterative strategy which builds successive motifs through comparison to a dynamic statistical background.
iMotifs is a graphical motif analysis environment for the Apple Mac computers (Leopard or later).It allows visualization of annotated sequence motifs and scored motif hits in sequences.
Bioinformatics. 2013 Jul 1;29(13):1696-7. doi: 10.1093/bioinformatics/btt248. Epub 2013 May 16. MEME-LaB: motif analysis in clusters.
Brown P, Baxter L, Hickman R, Beynon J, Moore JD, Ott S.
RASMOT-3D PRO searches in protein structure files for proteins possessing a group of residues in a topology similar to that adopted by a 3D motif given in input.
Nucleic Acids Res. 2009 Jul;37(Web Server issue):W459-64. doi: 10.1093/nar/gkp304. Epub 2009 May 5. RASMOT-3D PRO: a 3D motif search webserver.
Debret G1, Martel A, Cuniasse P.
DRIM (Discovery of Rank Imbalanced Motifs) is a tool for discovering short motifs in a list of nucleic acid sequences. DRIM was originally developed for DNA sequences and successfully applied on ChIP-chip and CpG methylation data. The current version has enhanced functionality and can be applied for both DNA and RNA. This new version was used to predict UTR motifs and Splicing Factor binding motifs based on RIP-Chip or CLIP data.
From a mathematical point of view, DRIM identifies subsequences that tend to appear at the top of the list more often than in the rest of the list. The definition of TOP in this context is flexible and driven by the data. Explicitly – DRIM identifies a threshold at which the statistical difference between top and rest is maximized. An exact p-value for the optimized event is also provided.
CSTP is a computational tool to predict the TF-target regulation with expression data based on a philosophy of guilt by association. Different from other tools, CSTP does not insist on clear TF binding site in the promoters of target genes.The expression information of genes allows prediction of CSTP to be condition-specific or tissue-specific