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DNA motif comparison software tools | Genome annotation

The growth of motif databases such as JASPAR, TRANSFAC  and a protein-binding microarray (PBM) motif database named UniPROBE spurred the development of new tools designed to allow researchers to test whether the motif returned by a motif finder…
Matcompare
Desktop

Matcompare

Provides a method for comparisons. MatCompare is a standalone software which…

Provides a method for comparisons. MatCompare is a standalone software which aims to detect similarities between position frequency matrices (PFMs) profiles and transcription factor binding site…

MoSBAT
Web
Desktop

MoSBAT Motif Similarity Based on Affinity of Targets

An approach for measuring the similarity of motifs by computing their affinity…

An approach for measuring the similarity of motifs by computing their affinity profiles across a large number of random sequences. We show that MoSBAT successfully associates de novo ChIP-seq motifs…

RSAT
Desktop
Web

RSAT Regulatory Sequence Analysis Tools

A modular software suite for the analysis of cis-regulatory elements in genome…

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)…

Tomtom
Web

Tomtom

Compares one or more motifs against a database of known motifs. Tomtom ranks…

Compares one or more motifs against a database of known motifs. Tomtom ranks the motifs in the database and produces an alignment for each significant match. The tool is part of the MEME Suite online…

BLiC
Desktop

BLiC Bayesian Likelihood 2-Components

Processes the set of DNA motifs into a set of reliable non-redundant motifs.…

Processes the set of DNA motifs into a set of reliable non-redundant motifs. BLiC is a large-scale analysis pipeline of DNA motif sets. This pipeline is designed for analysis following concurrent…

DiffLogo
Desktop

DiffLogo

A freely available, extensible, and user-friendly R package for visualizing…

A freely available, extensible, and user-friendly R package for visualizing motif differences. DiffLogo is capable of showing differences between DNA motifs as well as protein motifs in a pair-wise…

iMotifs
Desktop

iMotifs

A graphical motif analysis environment that allows visualization of annotated…

A graphical motif analysis environment that allows visualization of annotated sequence motifs and scored motif hits in sequences. iMotifs also offers motif inference with the sensitive NestedMICA…

MATLIGN
Web
Desktop

MATLIGN

Allows to cluster and compare DNA sequence motifs. MATLIGN can automatically…

Allows to cluster and compare DNA sequence motifs. MATLIGN can automatically convert consensus sequences (CSs) into position frequency matrices (PFMs) and treats all input motifs in a similar manner.…

m2match
Web

m2match

Searches for pairwise ungapped local alignments between Position-specific…

Searches for pairwise ungapped local alignments between Position-specific Frequency Matrices (PFMs). m2match determines if a custom matrix represents a novel, newly identified motif. It can compare a…

STAMP
Web

STAMP

Designs to support the study of DNA-binding motifs. STAMP may be used to query…

Designs to support the study of DNA-binding motifs. STAMP may be used to query motifs against databases of known motifs; the software aligns input motifs against the chosen database (or alternatively…

MACRO-APE
Desktop
Web

MACRO-APE Matrix Comparison by Approximate P-value Estimation

Allows computing the Jaccard similarity measure for a pair of Position Weight…

Allows computing the Jaccard similarity measure for a pair of Position Weight Matrices (PWMs) with given threshold values. MACRO-APE allows scanning a given collection of matrices for PWMs similar to…

SPIC
Desktop

SPIC Similarity with Position Information Contents

Serves for column-to-column motif comparison. SPIC is a similarity metric based…

Serves for column-to-column motif comparison. SPIC is a similarity metric based on column information contents. It calculates a score between the position-specific scoring matrix (PSSM) multiplied by…

motifmatchr
Desktop

motifmatchr

Permits fast motif matching. motifmatchr is a package designed for analyzing…

Permits fast motif matching. motifmatchr is a package designed for analyzing many sequences and many motifs to find which sequences contain which motifs. This method is designed specifically for the…

twofeat
Desktop

twofeat

Finds neighbouring pairs of specified features in one or more input sequences.…

Finds neighbouring pairs of specified features in one or more input sequences. twofeat is an Emboss tool. Each feature may be specified by type, name, sense, score, tag/value pairs etc. Their…

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