TFM (Transcription Factor Matrices) is a software suite for identifying and analyzing transcription factor binding sites modeled by weighted matrices, such as Position Weight Matrices and Position Specific Scoring Matrices. It is of great interest to decipher regulatory regions in DNA sequences and elucidate transcriptional regulation.
TFM-Explorer
This program analyses regulatory regions of eukaryotic genomes by looking at local overrepresentation and conservation across species. Available genomes: human, mouse, rat, chicken, drosophila.
TFM-Scan
This is a basic tool for locating transcription factor binding sites modeled by weighted matrices. It relies on matrix indexing, and is extremely efficient on long genomic sequences.
TFM-Pvalue
Fast and accurate calculation of P-values for weighted matrices. It computes both the score threshold associated to a given P-value, and the P-value associated to a given score threshold.
TFM-CUDA
TFM-CUDA provides parallel implementations of some features of TFM-Scan and TFM-Pvalue for NVIDIA GPUs