scan-x is a software tool designed to find motifs within any sequence data set. The first large scale scan was performed using all available human, mouse, fly and yeast phosphorylation and acetylation data to perform a scan for undiscovered modification sites.
SIOMICS is a software developed to de novo identify motifs in large sequence datasets such as those from ChIP-seq experiments. The output of the software is the ranked motifs and motif modules (significantly co-occurring motif combinations). The statistical evaluation of the predicted motifs and motif modules is also provided.
MultiMotif is a tool for finding statistically significant labeled motifs in multi-relational networks with analytically derived p-values. MultiMotif uses a custom version of RI algorithm for counting occurrences of labeled motifs in a graph and implements an analytical model to assess motifs significance without generating random graphs. MultiMotif works on both directed and undirected networks and handle non-induced labeled motifs.
Micale G, Pulvirenti A, Ferro A, Giugno R, Shasha D (2019).
Fast methods for finding significant motifs on labelled multi-relational networks.
Journal of Complex Networks, doi:10.1093/comnet/cnz008
FlashMotif is software for finding statistically significant colored motifs with analytically derived p-values. FlashMotif uses the GLabTrie algorithm for counting occurrences of colored motifs in a graph and implements an analytical model to assess motifs significance without generating random graphs. FlashMotif works on both directed and undirected networks and can handle induced and non-induced injective and multiset topological colored motifs with color-topology dependency or independency.
WebPSSM (position-specific scoring matrices ) is a bioinformatic tool for predicting HIV-1 coreceptor usage from amino acid or nucleotide sequences of the third variable loop (V3) of the envelope gene. When a nucleotide sequence is entered, it will be translated to amino acid sequence first. If a nucleotide sequence contains ambiguous bases, it will be translated to all possible amino acid sequences.
PEnG-motif is an open-source software package for searching statistically overrepresented motifs (position specific weight matrices, PWMs) in a set of DNA sequences.
The Dragon PolyA Spotter is a tool to predict polyadenylation signals variants in primary human genomic sequences. The application displays predicted polyA signal variants and their positions in each submitted fasta sequence.
Element is a web-based tool that identifies over-represented motifs across groups of promoters. Numerous plant genomes are already available online to be run against. If you don’t see your genome of interest, feel free to suggest that we add it.