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DNA motif enrichment software tools | Genome annotation

Motif enrichment analysis tests known motifs for enrichment in a set of user-provided sequences. This approach is more sensitive than motif discovery, but motif enrichment analysis is limited to detecting enrichment of motifs contained in the…
i-cisTarget
Web

i-cisTarget

An integrative genomics method for the prediction of regulatory features and…

An integrative genomics method for the prediction of regulatory features and cis-regulatory modules in Human, Mouse, and Fly. ii-cisTarget enables: (i) to detect transcription factor motifs in a set…

RTFBSDB
Desktop

RTFBSDB

A unified framework that integrates a database of more than 65,000…

A unified framework that integrates a database of more than 65,000 transcription factors (TFs) binding motifs with tools to easily and efficiently scan target genome sequences. Rtfbsdb clusters…

CentriMo
Desktop
Web

CentriMo

Identifies known or user-provided motifs that show a significant preference for…

Identifies known or user-provided motifs that show a significant preference for particular locations in your nucleotide sequences. CentriMo can also show if the local enrichment is significant…

CENTDIST
Web

CENTDIST

A web-application for identifying co-localized transcription factors around…

A web-application for identifying co-localized transcription factors around ChIP-seq peaks. In comparison to current co-motif scanning programs, CENTDIST does not require the input of any…

Clover
Desktop

Clover Cis-eLement OVERrepresentation

A program for identifying functional sites in DNA sequences. If you give it a…

A program for identifying functional sites in DNA sequences. If you give it a set of DNA sequences that share a common function, clover will compare them to a library of sequence motifs (e.g.…

SpaMo
Desktop
Web

SpaMo Spaced Motif Analysis Tool

Identifies significantly enriched spacings in a set of sequences between a…

Identifies significantly enriched spacings in a set of sequences between a primary motif and each motif in a set of secondary motifs. Typically, the input sequences are centered on ChIP-seq peaks,…

JFreq
Desktop

JFreq Java Word Frequencies

Provides a front end to Schbath’s R’MES. JFreq finds the expected and…

Provides a front end to Schbath’s R’MES. JFreq finds the expected and actual frequencies of short nucleotide sequences, or words, using a Markov model to control for the effects of base…

GOMo
Desktop
Web

GOMo Gene Ontology for Motifs

Scans all promoters using nucleotide motifs you provide to determine if any…

Scans all promoters using nucleotide motifs you provide to determine if any motif is significantly associated with genes linked to one or more genome ontology (GO) terms. The significant GO terms can…

PASTAA
Desktop
Web

PASTAA

A method for detecting transcriptions factors associated with functional…

A method for detecting transcriptions factors associated with functional categories, which utilizes the prediction of binding affinities of a transcription factor (TF) to promoters. This binding…

AME
Desktop
Web

AME Analysis of Motif Enrichment

Perform standard (non-local) motif enrichment analysis. This threshold-free…

Perform standard (non-local) motif enrichment analysis. This threshold-free linear regression method works well on ChIP-chip data. Methods using data-driven threshold determination can perform poorly…

MoSEA
Desktop

MoSEA Motif Scan and Enrichment Analysis

Provides a pipeline that offers enrichment analysis and motif scans. MoSEA…

Provides a pipeline that offers enrichment analysis and motif scans. MoSEA permits to: (i) extract fasta sequences from given bed file coordinates, (ii) scan fasta sequences for given motifs, and…

R'MES
Desktop

R'MES

Detects which motifs of a given length occur with an exceptional frequency in a…

Detects which motifs of a given length occur with an exceptional frequency in a given DNA sequence. R’MES finds the expected and actual frequencies of short nucleotide sequences, or words, using a…

G T A T C G C T A
Genomatix…
Desktop

Genomatix Software Suite

Allows analysis of genomic data. Genomatix Software Suite is a software that…

Allows analysis of genomic data. Genomatix Software Suite is a software that allows analysis of gene regulation and expression, generation and evaluation of network and pathways and visualization of…

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