The main question R'MES addresses is "does this motif occur in that biological sequence with an expected frequency?" In other words, can we observe it so many times, or so few times, just by chance? Usually, when the answer is no, such a motif is a candidate to have a particular biological meaning; only a candidate: statistical significance is not equivalent to biological significance.

Java Word Frequencies (JFreq) is a front end to Schbath's R'MES

PhyloGibbs is an algorithm for discovering regulatory sites in a collection of DNA sequences, including multiple alignments of orthologous sequences from related organisms. Many existing approaches to either search for sequence-motifs that are overrepresented in the input data, or for sequence-segments that are more conserved evolutionary than expected. PhyloGibbs combines these two approaches and identifies significant sequence-motifs by taking both over-representation and conservation signals into account.

In biological sequence analysis, position specific scoring matrices (PSSMs) are widely used to represent sequence motifs. We present a new non-heuristic algorithm, called ESAsearch, to efficiently find matches of such matrices in large databases. PoSSuMsearch Fast and Sensitive Matching of Position Specific Scoring Matrices Using Enhanced Suffix Arrays

software tool which screens query sequences against a reference collection of repeats

The REPuter program family provides state of the art software solutions to compute and visualize repeats in whole genomes or chromosomes. REPuter computes all maximal duplications and reverse, complemented and reverse complemented repeats in a DNA input sequence.

jPREdictor was designed for the prediction of cis-regulatory elements, for which short motifs (protein binding sites on the DNA) are known. Using these motifs, it is possible to search them on sequences, to weight them by applying a positive or negative training set (model or background, respectively) and to score a sequence.

TFM (Transcription Factor Matrices) is a software suite for identifying and analyzing transcription factor binding sites in DNA sequences.

SeqVISTA: A Graphical Tool for Sequence Feature Visualization and Comparison. SeqVISTA presents a holistic, graphical view of features annotated on nucleotide or protein sequences. This interactive tool highlights the residues in the sequence that correspond to features chosen by the user, and allows easy searching for sequence motifs or extraction of particular subsequences. SeqVISTA is able to display results from diverse sequence analysis tools in an integrated fashion, and aims to provide much-needed unity to the bioinformatics resources scattered around the Internet.

Allows to check your sequence against known regulatory sequences, and also allows one to query the regulatory sequence database for specific motifs.

CpG Islands searches for CpG islands in a DNA sequence using the method described by Gardiner-Garden and Frommer (1987).

The CpG island searcher screens for CpG islands which meet the criteria selected below in submitted DNA sequences.

CpG Island finder and plotting tool. An EMBOSS tool at the EBI that detects regions of genomic sequences rich in the CpG pattern.

Compares two DNA sequences assuming colinear blocks, ideal for promoters.

Compares two DNA sequences allowing for inversions and translocations, ideal for promoters.

QGRS Mapper is a software program that generates information on composition and distribution of putative Quadruplex forming G-Rich Sequences (QGRS) in nucleotide sequences. It is also designed to handle the analysis of mammalian pre-mRNA sequences, including that are alternatively processed (alternatively spliced or alternatively polyadenylated). QGRS Mapper is based on published algorithms for recognition and mapping of putative QGRS.

UTRscan looks for UTR functional elements by searching through user submitted sequence data for the patterns defined in the UTRsite collection.

UTRSite is a collection of functional sequence patterns located in 5' or 3' UTR sequences.