DNA motif finding software tools | Genome annotation
De-novo motif search is a frequently applied bioinformatics procedure to identify and prioritize recurrent elements in sequences sets for biological investigation, such as the ones derived from high-throughput differential expression experiments. Several algorithms have been developed to perform motif search, employing widely different approaches and often giving divergent results.
Gives access to many free software tools for sequence analysis. EMBOSS aims to serve the molecular biology community. It permits the creation and the release of software in an open source spirit. This tool is useful for sequence analysis into a seamless whole. It is free of charge and is available in open source.
Discovers novel, ungapped motifs (recurring, fixed-length patterns) in your nucleotide or protein sequences (sample output from sequences). MEME splits variable-length patterns into two or more separate motifs. MEME is part of the MEME Suite online platform.
A modular software suite for the analysis of cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery, appropriate to genome-wide data sets like ChIP-seq, (ii) transcription factor binding motif analysis (quality assessment, comparisons and clustering), (iii) comparative genomics and (iv) analysis of regulatory variations.
Allows users to process genomic loci with an emphasis on datasets consisting of ChIP-derived signal peaks. PeakAnalyzer is an open source software composed of two main functions: (i) PeakSplitter that aims to improve individual subpeaks’ analysis, and (ii) PeakAnnotator aims to provide an automated annotation of experimental results. The components can be executed simultaneously through a graphic interface or separately in command-line mode.
Examines the upstream region of genes in the same gene expression pattern group and looks for regulatory sequence motifs. BioProspector uses zero to third-order Markov background models whose parameters are either given by the user or estimated from a specified sequence file. The significance of each motif found is judged based on a motif score distribution estimated by a Monte Carlo method. In addition, BioProspector modifies the motif model used in the earlier Gibbs samplers to allow for the modeling of gapped motifs and motifs with palindromic patterns.
Investigates biological patterns. PatScan is an application based on the use of an expressive pattern language to detect predetermined DNA and protein sequence patterns. Users have the possibility to look for repeats, hairpins, stem loops or pseudoknots. The application can be run under a command-line interface for researchers with advanced skills or as a simplified web interface exploiting a drag & drop system.
Discovers short nucleotide or peptide sequences and patterns using Arabidopsis thaliana sequence datasets hosted in The Arabidopsis Information Resource (TAIR). PatMatch is a web application performing searches up to 20 residues and that supports both exact or approximate sequence matches. It also provides options allowing users to specify the number of hits that have to be returned or on which strand searching have to be run.