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DNA motif location detection software tools | Genome annotation

A motif is a short DNA or protein sequence that contributes to the biological function of the sequence in which it resides. Over the past several decades, many computational methods have been described for identifying, characterizing and searching…
Paraclu
Desktop

Paraclu

Intends to detect clusters from data attached to sequence. Paraclu identifies…

Intends to detect clusters from data attached to sequence. Paraclu identifies clusters in genomic data and uses a density parameter for reporting the segments of each chromosome. It allows users to…

Cluster-Buster
Web
Desktop

Cluster-Buster

Allows to find clusters of pre-specified motifs in DNA sequences. The…

Allows to find clusters of pre-specified motifs in DNA sequences. The Cluster-Buster program permits to analyze multiple sequences at once, and especially sequences longer than 100 kb. The main…

P-Match
Web
Desktop

P-Match

Identifies transcription factor binding sites (TFBS) in DNA sequences. P-Match…

Identifies transcription factor binding sites (TFBS) in DNA sequences. P-Match is based on simultaneous use of a positional weight matrix (PWM) and a set of aligned TFBS. The schema used for…

TFBSTools
Desktop

TFBSTools

An R/Bioconductor package for the analysis and manipulation of transcription…

An R/Bioconductor package for the analysis and manipulation of transcription factor binding sites and their associated transcription factor profile matrices. TFBStools provides a toolkit for handling…

ConTra
Web

ConTra conserved TFBSs

VIB Bioinformatics Core, Zwijnaarde-Ghent, Belgium; VIB-UGent Center for…

VIB Bioinformatics Core, Zwijnaarde-Ghent, Belgium; VIB-UGent Center for Inflammation Research, Zwijnaarde-Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University,…

motifcounter
Desktop

motifcounter

Provides functionality to compute the statistics related with motif matching…

Provides functionality to compute the statistics related with motif matching and counting of motif matches in DNA sequences. motifcounter provides functions to investigate the per-position and…

MCAST
Desktop
Web

MCAST Motif Cluster Alignment and Search Tool

Uses a motif-based hidden Markov model to scan for clusters of motifs. Its key…

Uses a motif-based hidden Markov model to scan for clusters of motifs. Its key features include a scoring scheme based on p-values and a method for calibrating the resulting scores to obtain…

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…

COMPASSS
Desktop

COMPASSS COMplex PAttern of Sequence Search Software

Detects presence of complex elements by mining whole genomes. COMPASSS is based…

Detects presence of complex elements by mining whole genomes. COMPASSS is based on Wu-Manber multiple pattern matching algorithm and intends to identify motifs from an entire sequence. The software…

OTFBS
Web

OTFBS Over-represented Transcription Factor Binding Site Prediction Tool

A method to identify over‐represented oligonucleotides in the promoters of a…

A method to identify over‐represented oligonucleotides in the promoters of a same protein family or a group of functionally related genes with the TRANSFAC matrices. These oligonucleotides are…

Pscan
Desktop
Web

Pscan

Scans a set of sequences (e.g. promoters) from co-regulated or co-expressed…

Scans a set of sequences (e.g. promoters) from co-regulated or co-expressed genes with motifs describing the binding specificity of known transcription factors and assesses which motifs are…

MotifViz
Web

MotifViz

An interactive web server for three motif discovery programs, Clover, Rover and…

An interactive web server for three motif discovery programs, Clover, Rover and Motifish, covering most available flavors of algorithms for achieving this goal. For comparison, the simple…

PWMEnrich
Desktop

PWMEnrich

Assesses the enrichment of motif hits in a sequence (or group of sequences)…

Assesses the enrichment of motif hits in a sequence (or group of sequences) compared to a genomic background. PWMEnrich offers high-level functions to scan for DNA motif occurrences. Users can…

seqPattern
Desktop

seqPattern

Visualises oligonucleotide patterns and sequence motifs occurrences across a…

Visualises oligonucleotide patterns and sequence motifs occurrences across a large set of sequences centred at a common reference point and sorted by a user defined feature. seqPattern is an R…

FIMO
Desktop
Web

FIMO Find Individual Motif Occurrences

A software tool for scanning DNA or protein sequences with motifs described as…

A software tool for scanning DNA or protein sequences with motifs described as position-specific scoring matrices. The FIMO algorithm identifies all individual motif occurrences and is the method of…

GLAM2Scan
Desktop
Web

GLAM2Scan

Searches sequences for matches to gapped DNA or protein GLAM2 motifs. GLAM2Scan…

Searches sequences for matches to gapped DNA or protein GLAM2 motifs. GLAM2Scan is similar to FIMO but is designed to accept GLAM2 motifs; hence, the resulting motif matches may contain insertions…

TFM-Explorer
Desktop
Web

TFM-Explorer Transcription Factor Matrix Explorer

A program for analysing regulatory regions in eukaryotic genomes. TFM-Explorer…

A program for analysing regulatory regions in eukaryotic genomes. TFM-Explorer takes a set of coregulated gene sequences, and searches for locally overrepresented transcription factor binding sites.…

MAST
Desktop
Web

MAST Motif Alignment & Search Tool

Searches sequences for matches to a set of nucleotide or protein motifs, and…

Searches sequences for matches to a set of nucleotide or protein motifs, and sorts the sequences by the best combined match to all motifs. MAST algorithm is sequence oriented and assigns each…

G T A T C G C T A
pybio
Desktop

pybio

Permits users to proceed to basic genomics operations. pybio offers motif…

Permits users to proceed to basic genomics operations. pybio offers motif sequence searches functions. It can classify alternative polyadenylation site-pair.

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…

F-Match
Web

F-Match

Identifies statistically over-represented transcription factor binding sites…

Identifies statistically over-represented transcription factor binding sites (TFBS) in a set of sequences. F-Match compares the number of sites found in a query sequence set against the background…

G T A T C G C T A
HTS-Tools
Desktop

HTS-Tools

Tools and scripts for basic analysis of NGS data. This is a collection of tools…

Tools and scripts for basic analysis of NGS data. This is a collection of tools for the analysis of NGS data (ChIP-Seq, RNA-Seq, methylation analysis and motif scanning). They are written mostly in…

GFScan
Desktop

GFScan Gene FamilyScan

Recognizes new members of a gene family. GFScan searches genomic DNA sequence…

Recognizes new members of a gene family. GFScan searches genomic DNA sequence directly thanks to a representative DNA motif of a gene family. It can construct the genomic motif automatically. This…

UpCoT
Web
Desktop

UpCoT

Predicts cis-regulatory elements using phylogenetic foot printing from…

Predicts cis-regulatory elements using phylogenetic foot printing from microbial genomes. UpCoT is able to execute prediction of bidirectional best hits, clusters of transcriptional units (tgCoTs)…

CORE_TF
Web

CORE_TF Conserved and Over-REpresented Transcription Factor binding sites

Identifies common transcription factor binding sites in promoters of…

Identifies common transcription factor binding sites in promoters of co-regulated genes. To improve upon existing binding site predictions, the tool searches for position weight matrices from the…

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