GIMSAN: motif-finder with biologically realistic and reliable statistical significance analysis

Details application of UniDip to the problem of biologic motif discovery. We find that UniDip is able to preprocess DNA sequences such that MEME is able to find motifs 70% faster.

Evaluate de novo motif finding tools

The repository stores files that were used to perform Tbx5 transcription factor analysis with house mouse heart cells.

Classify transcriptional factor motifs into true motifs and false motifs

A tool to search for motifs within the whole genome or regions of interest

MapReduce-based Algorithm for Motif Search

Take the list of motif occurrences output by FIMO (a MEME suite tool) and convert it into the Instances format used by MotifSuite tools.

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

Docker image to easy run meme suite in web mode http://meme-suite.org/

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

Gibbs 3.2 formerly located at http://ccmbweb.ccv.brown.edu/gibbs/gibbs.html

Re-implementation and some initialization analysis of Multiple EM for Motif Elicitation (MEME).

Bioinformatics- High-throughput data Analysis project

A contrast motif discovery approach for analyzing discrete sequences.

motif locator for plant resistance genes.

Transceiver Framework: A framework for concurrent multi stage processing of data & MDP: An online motif detector and predictor embedded in the transceiver framework.

A package-like tool that analyzes protein sequences, categorizes a protein of interest into one of two groups, predicts secondary structure based on dihedral angles/Ramachandran plots and Chou and Fasman's statistical propensity method, and does pattern search by Naive, KMP, and Bayer-Moore