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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.…
G T A T C G C T A
Weeder
Desktop
Web

Weeder

Falls into the motif enumeration family of motif discovery tools in which the…

Falls into the motif enumeration family of motif discovery tools in which the occurrence of motifs in the query sequences are counted and, in this case, compared to a pre-calculated set of genome…

AlignACE
Desktop
Web

AlignACE Aligns Nucleic Acid Conserved Elements

A Gibbs sampling algorithm for identifying motifs that are over-represented in…

A Gibbs sampling algorithm for identifying motifs that are over-represented in a set of DNA sequences. When used to search upstream of apparently coregulated genes, AlignACE finds motifs that often…

MDscan
Desktop
Web

MDscan Motif Discovery scan

A computational method that examines the ChIP-array-selected sequences and…

A computational method that examines the ChIP-array-selected sequences and searches for DNA sequence motifs representing the protein-DNA interaction sites. MDscan combines the advantages of two…

Improbizer
Desktop
Web

Improbizer

Searches for motifs in DNA or RNA sequences that occur with improbable…

Searches for motifs in DNA or RNA sequences that occur with improbable frequency (to be just chance) using a variation of the expectation maximization (EM) algorithm. As a background (null) model it…

The Gibbs…
Desktop
Web

The Gibbs Motif Sampler

A software package for locating common elements in collections of biopolymer…

A software package for locating common elements in collections of biopolymer sequences. Gibbs Motif Sampler includes several features that are designed specifically for locating TFBS in unaligned DNA…

FIRE
Desktop

FIRE Finding Informative Regulatory Elements

Infers motifs from gene expression data. FIRE allows the discovery of DNA and…

Infers motifs from gene expression data. FIRE allows the discovery of DNA and RNA motifs that show generic dependency with diverse aspects of gene expression. It takes into account differential…

EMD
Desktop

EMD Ensemble Motif Discovery

Supplies an ensemble algorithm for regulatory site motif discovery. EMD is…

Supplies an ensemble algorithm for regulatory site motif discovery. EMD is composed of five algorithms which are run several times independently. Their results are summarized basically by majority.…

DynaMIT
Desktop

DynaMIT Dynamic Motif Integration Toolkit

An extremely flexible platform allowing to identify motifs employing multiple…

An extremely flexible platform allowing to identify motifs employing multiple algorithms, integrate them by means of a user-selected strategy and visualize results in several ways; furthermore, the…

cooccurNet
Desktop

cooccurNet

Facilitates easy use of the co-occurrence network model. cooccurNet includes…

Facilitates easy use of the co-occurrence network model. cooccurNet includes functionalities of constructing and analyzing co-occurrence networks, as well as calculating the extent of co-occurrence…

Ori-Finder 1
Web
Desktop

Ori-Finder 1

Identifies replication origin (oriCs) in bacterial genomes. Ori-Finder 1 is an…

Identifies replication origin (oriCs) in bacterial genomes. Ori-Finder 1 is an online system based on an integrated method comprising the analysis of base composition asymmetry using the Z-curve…

G T A T C G C T A
SCOPE
Web

SCOPE Suite for Computational identification Of Promoter Elements

An ensemble of programs aimed at identifying novel cis-regulatory elements from…

An ensemble of programs aimed at identifying novel cis-regulatory elements from groups of upstream sequences. SCOPE motif finder uses an ensemble of three programs behind the scenes to identify…

DiRE
Web

DiRE Distance Regulatory Elements of co-regulated genes

Allows users to predict distant regulatory elements in higher eukaryotic…

Allows users to predict distant regulatory elements in higher eukaryotic genomes. DiRE provides computational means to investigate regulatory features of any user-submitted dataset of genes. It…

sequence-shape
Desktop

sequence-shape

Enables accurate and efficient modelling and prediction of transcription factor…

Enables accurate and efficient modelling and prediction of transcription factor (TF)-DNA binding affinities. sequence-shape uses kernel functions to measure similarity between DNA sequences and…

InMoDe
Desktop

InMoDe Intra-Motif Dependencies

A collection of seven tools for learning, leveraging, and visualizing…

A collection of seven tools for learning, leveraging, and visualizing intra-motif dependencies within DNA binding sites and similar functional nucleotide sequences. Learned inhomogeneous parsimonious…

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…

iOri-Human
Web

iOri-Human

Identifies human origin of replication. iOri-Human reflects the global sequence…

Identifies human origin of replication. iOri-Human reflects the global sequence patterns in DNA as well as its local sequence patterns through the pseudo nucleotide composition that 96…

iROS-gPseKNC
Web

iROS-gPseKNC

Incorporates the dinucleotide position-specific propensity information into the…

Incorporates the dinucleotide position-specific propensity information into the general pseudo nucleotide composition and uses the random forest classifier. iROS-gPseKNC can be used to identify the…

discovering-cse
Desktop

discovering-cse

A statistically rigorous framework for the discovery of motifs that induces…

A statistically rigorous framework for the discovery of motifs that induces sequencing errors. Discovering-cse detects the motifs and aggregates information at matching positions to identify…

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)…

PatternBranchin…
Desktop

PatternBranching/ProfileBranching

Provides a method to detect motif space from sample strings.…

Provides a method to detect motif space from sample strings. PatternBranching/ProfileBranching is composed of two algorithms: (i) PatternBranching aims to define motif space from the space of motif…

Oracle…
Desktop

Oracle Database 10g

Offers a range of improved data management and data sharing features that can…

Offers a range of improved data management and data sharing features that can support the biology domain. Oracle Database 10g provides a distributed data architecture. It allows users to write…

Insignia
Web

Insignia

Identifiesan exhaustive set of accurate DNA signatures for any set of target…

Identifiesan exhaustive set of accurate DNA signatures for any set of target genomes, and screens these signatures against a comprehensive background that includes all sequenced bacteria and viruses,…

Slim
Desktop
Web

Slim Sparse local inhomogeneous mixture

Combines putative dependency structures in a weighted manner allowing for…

Combines putative dependency structures in a weighted manner allowing for numerical optimization of dependency structure and model parameters simultaneously. We find that Slim models yield a…

MARS
Web

MARS Motif Assessment and Ranking Suite

A web server hosting a suite of tools that make position weight matrix (PWM)…

A web server hosting a suite of tools that make position weight matrix (PWM) motif evaluation and ranking techniques accessible. MARS is supported by a database of benchmark data and PWM models. This…

FIDDLE
Desktop

FIDDLE Flexible Integration of Data with Deep LEarning

A framework that learns a unified rich representation by exploiting synergistic…

A framework that learns a unified rich representation by exploiting synergistic interactions within and across datasets. FIDDLE comprises ConvNet modules for individual datasets and combines under a…

MOODS
Desktop

MOODS Motif Occurrence Detection Suite

Uses for motif matching to deal with high-order PWMs and variants in sequences.…

Uses for motif matching to deal with high-order PWMs and variants in sequences. MOODS is a suite of algorithms for matching position weight matrices (PWM) against DNA sequences, featuring advanced…

G T A T C G C T A
DeFCoM
Desktop

DeFCoM Detecting Footprints Containing Motifs

A supervised learning based footprint prediction framework. DeFCoM was designed…

A supervised learning based footprint prediction framework. DeFCoM was designed to capture variation in DNaseI signal within active footprints and unbound motif sites to enhance footprint…

PC-TraFF
Web

PC-TraFF Potentially Collaborating Transcription Factor finder

Detects interactions between homotypic and heterotypic transcription factor…

Detects interactions between homotypic and heterotypic transcription factor (TF) pairs using pointwise mutual information (PMI). PC-TraFF builds all possible transcription factor binding sites…

DistAMo
Web
Desktop

DistAMo Distribution Analysis of DNA Motifs

Determine motif distribution among single genes, groups of genes and the whole…

Determine motif distribution among single genes, groups of genes and the whole genome. DistAMo estimates motif distribution by the coding flexibility of the protein coding DNA. The application allows…

qPMS7
Web
Desktop

qPMS7

Tackles the qPMS problem on real data as well as challenging instances. qPMS7…

Tackles the qPMS problem on real data as well as challenging instances. qPMS7 is a framework for transcription factor-binding sites (TFBS) discovery developed for the qPMS problem and tested it on…

iFORM
Desktop

iFORM incorporating Find Occurrence of Regulatory Motifs

Analyses DNA sequences with transcription factors (TFs) motifs described as…

Analyses DNA sequences with transcription factors (TFs) motifs described as position weight matrices (PWMs). iFORM achieves higher accuracy and sensitivity by integrating five classical motif…

TELS
Desktop

TELS Transcribed Enhancer Landscape Search

Identifies predictive short motif signatures of transcribed enhancers (TrEn).…

Identifies predictive short motif signatures of transcribed enhancers (TrEn). TELS is a machine-learning algorithm that applies logistic regression (LR) coupled with dimensionality reduction…

SECOMO
Desktop

SECOMO SEquence COntext Modeler

Discovers redundant DNA sequences features. SECOMO is an unsupervised learning…

Discovers redundant DNA sequences features. SECOMO is an unsupervised learning model selects sequence context information in heterogeneous sequences and is useful to cluster sequences based in their…

LESMoN
Desktop

LESMoN Local Enrichment of Sequence Motifs in biological Networks

Identifies short sequence motifs whose containing sequences are unexpectedly…

Identifies short sequence motifs whose containing sequences are unexpectedly clustered in the network. LESMoN is a sequence motif discovery approach guided by a biological network. This method is…

Sequence2Vec
Desktop

Sequence2Vec

Models the transcription factor binding affinity landscape. Sequence2Vec…

Models the transcription factor binding affinity landscape. Sequence2Vec combines the strength of probabilistic graphical models, feature space embedding, and deep learning. It represents DNA binding…

ML2Motif
Desktop

ML2Motif

Finds driving motifs in real-world human splice-site data where ground truth…

Finds driving motifs in real-world human splice-site data where ground truth motifs are known. ML2Motif consists of two distinct methods: gPOIM and convex motifPOIM. gPOIM is a general measure of…

Cleaver
Desktop

Cleaver

Analyses restriction digestion of groups of orthologous DNA sequences…

Analyses restriction digestion of groups of orthologous DNA sequences simultaneously to allow identification of differences in restriction pattern among the fragments derived from different taxa.…

TreeMotif
Desktop

TreeMotif

Discovers longer and weaker motifs than by the existing methods. TreeMotif…

Discovers longer and weaker motifs than by the existing methods. TreeMotif converts the graphical representation of motifs into a tree-structured representation in which a tree that branches with…

MDDLogo
Web

MDDLogo

Applies maximal dependence decomposition (MDD) to cluster a group of aligned…

Applies maximal dependence decomposition (MDD) to cluster a group of aligned signal sequences into subgroups containing statistically significant motifs. MDDLogo has been demonstrated to accurately…

BEST
Desktop

BEST Binding-site Estimation Suite of Tools

Provides a platform for using and comparing different motif-finding programs…

Provides a platform for using and comparing different motif-finding programs for transcription factor binding site prediction. BEST includes a graphic user interface to integrate BioOptimizer with…

BLSSpeller
Desktop

BLSSpeller

Supports both alignment-free and alignment-based motif discovery in the…

Supports both alignment-free and alignment-based motif discovery in the promoter sequences of related species. Putative motifs are exhaustively enumerated as words over the IUPAC alphabet and…

regshape
Desktop

regshape

A transcription factor (TF)-generalized classifier based on local DNA shape…

A transcription factor (TF)-generalized classifier based on local DNA shape parameters that improves PWM-based transcription factor binding site (TFBS) prediction. regshape predicts whether a short…

Vocabulon
Desktop

Vocabulon

Allows you to reconstruct conserved words that appear in DNA sequence with a…

Allows you to reconstruct conserved words that appear in DNA sequence with a certain frequency. Vocabulon is based on a dictionary model description of DNA sequence and can be use both as a tool for…

TRAP
Desktop
Web

TRAP Transcription factor Affinity Prediction

Calculates the affinity of transcription factors for DNA sequences on the basis…

Calculates the affinity of transcription factors for DNA sequences on the basis of a biophysical model. This method has proven to be useful for several applications, including for determining the…

Melina II
Web

Melina II

A web-based tool for promoter analysis. Melina II shows potential DNA motifs in…

A web-based tool for promoter analysis. Melina II shows potential DNA motifs in promoter regions with a combination of several available programs, Consensus, MEME, Gibbs sampler, MDscan and Weeder,…

GLAM
Desktop

GLAM Gapless Local Alignment of Multiple sequences

A program for discovering functional motifs shared by a set of nucleotide…

A program for discovering functional motifs shared by a set of nucleotide sequences. Examples of functional motifs include transcription factor binding sites, mRNA splicing control elements, signals…

WebMOTIFS
Web

WebMOTIFS

Provides a web interface that facilitates the discovery and analysis of…

Provides a web interface that facilitates the discovery and analysis of DNA-sequence motifs. Used with the default settings, WebMOTIFS accurately identifies biologically relevant motifs from diverse…

YMF
Desktop

YMF

Identifies motifs (made of IUPAC symbols) that occur unusually often in a given…

Identifies motifs (made of IUPAC symbols) that occur unusually often in a given set of sequences. More specifically, YMF enumerates all motifs in the search space and is guaranteed to produce those…

XXmotif
Web

XXmotif

A de novo motif discovery method that is able to directly optimize the…

A de novo motif discovery method that is able to directly optimize the statistical significance of PWMs. XXmotif can also score conservation and positional clustering of motifs. The XXmotif server…

CMStalker
Desktop

CMStalker

Permits Composite Module detection. CMStalker is based on purely combinatorial…

Permits Composite Module detection. CMStalker is based on purely combinatorial ideas. It explores the space state of possible solutions by progressively relaxing some (internal) parameters. This tool…

ExactSearch
Web

ExactSearch

Facilitates the searching of DNA motifs in either custom sequences or the…

Facilitates the searching of DNA motifs in either custom sequences or the proximal promoters or 3′ UTR of 50 genome-sequenced plant species using suffix-tree algorithm. ExactSearch is a…

Ori-Finder 2
Web

Ori-Finder 2

Predicts replication origins (oriCs) in archaeal genomes. Ori-Finder 2 is a web…

Predicts replication origins (oriCs) in archaeal genomes. Ori-Finder 2 is a web server which utilizes an integrated method to automatically predict the replication origins in archaeal genome…

MULTIPROFILER
Desktop

MULTIPROFILER

Outperforms other leading motif finding algorithms in a number of synthetic…

Outperforms other leading motif finding algorithms in a number of synthetic models. Moreover, it can be shown that in some previously studied motif models, MULTIPROFILER is capable of pushing the…

CREAD
Desktop

CREAD Comprehensive Regulatory Element Analysis and Discovery

A framework for studying regulatory elements in a genome. Currently focusing on…

A framework for studying regulatory elements in a genome. Currently focusing on patterns involved in transcriptional regulation, CREAD includes efficient tools for performing fundamental tasks in…

DME
Desktop

DME Discriminating Matrix Enumerator

A program that discovers transcription factor binding site motifs in nucleotide…

A program that discovers transcription factor binding site motifs in nucleotide sequences. DME identifies motifs, represented as position weight matrices, that are overrepresented in one set of…

CSTP
Web

CSTP Condition-Specific Target Prediction

A tool to predict condition-specific targets for transcription factors (TFs)…

A tool to predict condition-specific targets for transcription factors (TFs) from expression data measured by either microarray or RNA-seq. Based on the philosophy of guilt by association, CSTP…

GMACS
Desktop

GMACS

A genetic-k-medoids approach which allows motifs to move freely between…

A genetic-k-medoids approach which allows motifs to move freely between clusters at any point in the clustering process. GMACS is generally applicable to any DNA or protein motifs, can produce highly…

SeAMotE
Web

SeAMotE Sequence Analysis of Motifs Enrichment

An algorithm for discovery of regulatory regions in nucleic acid sequences.…

An algorithm for discovery of regulatory regions in nucleic acid sequences. SeAMotE provides (i) a robust analysis of high-throughput sequence sets, (ii) a motif search based on pattern occurrences…

Uniform…
Desktop

Uniform Projection Motif Finder

Provides a motif discovery problem algorithm. Uniform Projection Motif Finder…

Provides a motif discovery problem algorithm. Uniform Projection Motif Finder is derivated from the random projection algorithm but uses a greedy heuristic that approximately equalizes the coverage…

SMILE
Desktop

SMILE

Focuses on the detection of binding sites in DNA sequences. SMILE is a method…

Focuses on the detection of binding sites in DNA sequences. SMILE is a method that allows users to represent binding sites and is able to appear associated in a more or less constrained manner. This…

BCRANK
Desktop

BCRANK

Takes a ranked list of genomic regions as input and outputs short DNA sequences…

Takes a ranked list of genomic regions as input and outputs short DNA sequences that are over represented in some part of the list. BCRANK uses a heuristic search strategy. It was developed for…

SeqS
Desktop

SeqS Sequence Searcher

Can perform both search types on DNA and protein sequences. SeqS is an easy to…

Can perform both search types on DNA and protein sequences. SeqS is an easy to use Java-based tool that allows Fuzzy and Regular Expression searches on multiple sequences. It reads and uses sequences…

Motif Locator
Web

Motif Locator

Uses aligned set of DNA sequence motifs and finds similar motifs in the…

Uses aligned set of DNA sequence motifs and finds similar motifs in the analyzed sequence. Motif Locator uses position specific score matrix (PSSM) representation of the motif. The program takes as…

Pattern locator
Web
Desktop

Pattern locator

Finds local sequence patterns in long DNA sequences. Pattern Locator uses an…

Finds local sequence patterns in long DNA sequences. Pattern Locator uses an intuitive syntax for pattern description. It allows combinations of specific nucleotide sequences, direct and inverted…

PARSEC
Desktop

PARSEC PAtteRn Search and Contextualization

An open source platform for guided discovery, allowing localization and…

An open source platform for guided discovery, allowing localization and biological characterization of short genomic sites in entire eukaryotic genomes. PARSEC can search for a sequence or a…

MotifSuite
Desktop
Web

MotifSuite

Provides a platform for de novo regulatory motif detection using a stochastic…

Provides a platform for de novo regulatory motif detection using a stochastic motif detection algorithm with various motif assessment tools. The suite revolves around MotifSampler, a de novo motif…

Co-Bind
Desktop

Co-Bind COperative BINDing

An algorithm for discovering DNA target sites for cooperatively acting…

An algorithm for discovering DNA target sites for cooperatively acting transcription factors. Co-Bind utilizes a Gibbs sampling strategy to model the cooperativity between two transcription factors…

Tmod
Desktop

Tmod Toolbox of Motif Discovery

Provides a unified interface to ease the use of these programs and help users…

Provides a unified interface to ease the use of these programs and help users to understand the tuning parameters. The current version of Tmod integrates 12 widely used motif discovery programs:…

MotifVoter
Web

MotifVoter

A variance based ensemble method for discovery of binding sites. MotifVoter…

A variance based ensemble method for discovery of binding sites. MotifVoter uses 11 most common used individual basic motif finders as its component. In terms of sensitivity and precision, MotifVoter…

SPACE
Desktop

SPACE

Detects the target motif by first finding submotifs and then strategically…

Detects the target motif by first finding submotifs and then strategically compositing them using an efficient frequent submotif pattern-mining approach. In finding motif with generic spacers, this…

info-gibbs
Web

info-gibbs

A Gibbs sampling algorithm that efficiently optimizes the IC or the…

A Gibbs sampling algorithm that efficiently optimizes the IC or the log-likelihood ratio (LLR) of the motif while keeping computation time low. The method compares well with existing methods like…

SOMBRERO
Desktop
MoSDi
Desktop

MoSDi

Contains a lot of sequence analysis algorithms, including methods for 1) motif…

Contains a lot of sequence analysis algorithms, including methods for 1) motif statistics, e.g. compute the exact occurrence count distribution of a motif, 2) exact motif discovery: extraction of…

MotifCut
Desktop
Web

MotifCut

A graph-theoretic approach to motif finding leading to a convex optimization…

A graph-theoretic approach to motif finding leading to a convex optimization problem with a polynomial time solution. MotifCut takes as input DNA sequences in FASTA format and returns to the user a…

Seeder
Desktop

Seeder

A framework for DNA motif discovery. Seeder is designed for efficient and…

A framework for DNA motif discovery. Seeder is designed for efficient and reliable prediction of regulatory motifs in eukaryotic promoters. In order to generate DNA motifs, you need one positive set…

DECOD
Desktop

DECOD DECOnvolved Discriminative motif discovery

A tool for finding discriminative DNA motifs, i.e. motifs that are…

A tool for finding discriminative DNA motifs, i.e. motifs that are over-represented in one set of sequences but are depleted from another. Uses a k-mer count table and so its running time is…

SeSiMCMC
Desktop
Web

SeSiMCMC Sequence Similarities by Markov Chain Monte Carlo

Finds DNA motifs of unknown length and complicated structure, such as direct…

Finds DNA motifs of unknown length and complicated structure, such as direct repeats or palindromes with variable spacers in the middle in a set of unaligned DNA sequences. SeSiMCMC employs improved…

Consensus
Web

Consensus

The identification of MHC class II restricted peptide epitopes is an important…

The identification of MHC class II restricted peptide epitopes is an important goal in immunological research. Consensus provides access to predictions of peptide binding to MHC class II molecules.

MotifIndexer
Desktop

MotifIndexer

A comprehensive strategy for de novo identification of DNA regulatory motifs at…

A comprehensive strategy for de novo identification of DNA regulatory motifs at a genome level. MotifIndexer is based on word counting strategy. This comparative genomics method does not depend on…

likelihood-rati…
Desktop

likelihood-ratio-motifs

A method of DNA sequence motif discovery based on logistic regression and…

A method of DNA sequence motif discovery based on logistic regression and rigorous hypothesis testing. likelihood-ratio-motifs includes searching through DNA sequences to identify “motifs” that…

CodingMotif
Desktop

CodingMotif

Provides a theoretically and empirically-demonstrated advance for the detection…

Provides a theoretically and empirically-demonstrated advance for the detection of motifs over-represented in coding sequences. CodingMotif is a time algorithm and an enumerative method that identify…

NestedMICA
Desktop

NestedMICA

An open source protein motif discovery tool written in Java, is driven by a…

An open source protein motif discovery tool written in Java, is driven by a Monte Carlo technique called Nested Sampling. NestedMICA uses multi-class sequence background models to represent different…

MotifClick
Desktop

MotifClick

A graph-based polynomial-time algorithm for the prediction of cis-regulatory…

A graph-based polynomial-time algorithm for the prediction of cis-regulatory binding sites, in particular, those that have a similar nucleotide distribution to that of their background sequences. The…

Motif Sampler
Desktop
Web

Motif Sampler

A probabilistic de novo motif detection tool for DNA sequences upstream of…

A probabilistic de novo motif detection tool for DNA sequences upstream of coregulated genes from one species. Detection is done by means of a stochastic optimization strategy (a Gibbs sampling…

GADEM
Desktop

GADEM

An efficient method which combines spaced dyads and an expectation-maximization…

An efficient method which combines spaced dyads and an expectation-maximization (EM) algorithm. Candidate words (four to six nucleotides) for constructing spaced dyads are prioritized by their degree…

BayesMD
Desktop
Web

BayesMD

A flexible, fully Bayesian model for motif discovery consisting of motif,…

A flexible, fully Bayesian model for motif discovery consisting of motif, background and alignment modules. The Bayesian inference is carried out using a combination of exact marginalization and…

RISOTTO
Desktop

RISOTTO

Allows users to extract motifs with mismatches. RISOTTO takes in consideration…

Allows users to extract motifs with mismatches. RISOTTO takes in consideration single and structured motifs which are motifs composed of several disjoint single motifs placed at given distances from…

Logol
Desktop

Logol

Permits users to find a pattern in a nucleic or proteic sequence. Logol uses a…

Permits users to find a pattern in a nucleic or proteic sequence. Logol uses a grammar language matching technique to proceed. The user can specify constraints such as position, size, or length. It…

iCorr
Algorithm

iCorr

Detect origin of replication in prokaryotic and eukaryotic genomes. Converts…

Detect origin of replication in prokaryotic and eukaryotic genomes. Converts the genome sequence into a sequence of complex numbers by mapping the nucleotides used in the auto-correlation method.…

RestrictionMapp…
Web

RestrictionMapper

Finds restriction endonuclease cleavage sites in DNA sequences.…

Finds restriction endonuclease cleavage sites in DNA sequences. RestrictionMapper is a web site that supports linear and circular DNA and provides several ways to sort and filter output. It provides…

fuzznuc
Desktop

fuzznuc

Searches for patterns in nucleotide sequences. fuzznuc searches for a specified…

Searches for patterns in nucleotide sequences. fuzznuc searches for a specified PROSITE-style pattern. Such patterns are specifications of a length of sequence to be found. They can specify a search…

Mobydick
Web

Mobydick

Decomposes a set of DNA sequences into the most probable dictionary of motifs…

Decomposes a set of DNA sequences into the most probable dictionary of motifs or words. This method is applicable to any set of DNA sequences: for example, all upstream regions in a genome or all…

MEME
Desktop
Web

MEME Multiple Em for Motif Elicitation

Discovers novel, ungapped motifs (recurring, fixed-length patterns) in your…

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…

ANN-Spec
Web

ANN-Spec

A machine learning algorithm and its application to discovering un-gapped…

A machine learning algorithm and its application to discovering un-gapped patterns in DNA sequence. The approach makes use of an Artificial Neural Network and a Gibbs sampling method to define the…

BioProspector
Desktop

BioProspector

Examines the upstream region of genes in the same gene expression pattern group…

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…

KBERG
Dataset

KBERG KnowledgeBase for Estrogen Responsive Genes

Allows exploration of some of the genes’ functional properties and…

Allows exploration of some of the genes’ functional properties and complements the experimental-information-rich Estrogen Responsive Gene Database (ERGDB). KBERG permits identification of highly…

Comparative…
Web

Comparative genomics motif finding

Provides a motif discovery algorithm. Comparative genomics motifs finding is a…

Provides a motif discovery algorithm. Comparative genomics motifs finding is a comparative genomics approach using neither prior information about which genes might be coregulated nor a detailed…

CLIMP
Desktop

CLIMP Clustering Motifs via Maximal Cliques with Parallel Computing Design

Allows clustering of large-scale motif. CLIMP is able to gather the motifs that…

Allows clustering of large-scale motif. CLIMP is able to gather the motifs that belong to the same groups and to dissociate the motifs belonging to several groups. It contains a novel metric for…

MITRA
Desktop

MITRA MIsmatch TRee Algorithm

An approach for discovering composite signals. MITRA performs well for both…

An approach for discovering composite signals. MITRA performs well for both monad and composite patterns by presenting experiments over biological and synthetic data.

D-MATRIX
Web

D-MATRIX

Builds weight matrices based on user defined motif sequences and width.…

Builds weight matrices based on user defined motif sequences and width. D-MATRIX generates several types of matrices such as alignment, frequency and weight matrix. The software can also perform a…

C.U.R.F.F.
Desktop

C.U.R.F.F. Codon Usage regarding Restriction Finder

Detects possible restriction sites in both coding and non-coding DNA sequences…

Detects possible restriction sites in both coding and non-coding DNA sequences while regarding the codon bias use of the host organism. CURFF provides a codon optimizing function for the comparison…

Kangaroo
Desktop

Kangaroo

Facilitates a wide range of queries with no restriction on the length or…

Facilitates a wide range of queries with no restriction on the length or complexity of the query expression. Kangaroo is a web-based regular expression pattern-matching program that can search for…

ESPERR
Desktop

ESPERR Evolutionary and Sequence Pattern Extraction through Reduced Representations

Authorizes users to predict specific classes of functional elements and…

Authorizes users to predict specific classes of functional elements and cis-regulatory modules. ESPERR is a computational method that is developed to create a reduced representation for removing…

QuickScore
Web

QuickScore

Estimates probabilities of rare or frequent words in genomic texts based on an…

Estimates probabilities of rare or frequent words in genomic texts based on an exhaustive searching algorithm. QuickScore incorporates an extended consensus method allowing well-defined mismatches…

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