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Promoter detection software tools | Genome annotation

More and more genomes are being sequenced, and to keep up with the pace of sequencing projects, automated annotation techniques are required. One of the most challenging problems in genome annotation is the identification of the core promoter.Source…
FirstEF
Web

FirstEF First Exon Finder

A 5' terminal exon and promoter prediction program. FirstEF consists of…

A 5' terminal exon and promoter prediction program. FirstEF consists of different discriminant functions structured as a decision tree. The probabilistic models are optimized to find potential…

CpGpromoter
Desktop
Web

CpGpromoter

A program for a large-scale human promoter mapping using CpG islands.…

A program for a large-scale human promoter mapping using CpG islands. CpGpromoter is based on results of discriminant analysis between the promoter-associated CpG islands and non-associated ones. It…

PlantPAN
Web

PlantPAN Plant Promoter Analysis Navigator

Provides an informative resource for detecting transcription factor binding…

Provides an informative resource for detecting transcription factor binding sites (TFBSs), corresponding transcription factors (TFs), and other important regulatory elements (CpG islands and tandem…

NNPP
Web

NNPP Neural Network Promoter Prediction

Allows to predict variable spacing between functional binding sites, which is…

Allows to predict variable spacing between functional binding sites, which is known to play a key role in the transcription initiation process. The Neural Network Promoter Prediction is a method that…

NPLB
Desktop
Web

NPLB No Promoter Left Behind

An efficient, organism-independent method for characterizing such diverse…

An efficient, organism-independent method for characterizing such diverse architectures directly from experimentally identified genome-wide transcription start sites (TSSs), without relying on known…

PlantCARE
Dataset

PlantCARE

A database of plant cis-acting regulatory elements, enhancers and repressors.…

A database of plant cis-acting regulatory elements, enhancers and repressors. Regulatory elements are represented by positional matrices, consensus sequences and individual sites on particular…

PromoSer
Web

PromoSer

Facilitates extraction of user specified regions around the transcription start…

Facilitates extraction of user specified regions around the transcription start site of all annotated human, mouse or rat genes. The transcription start sites have been identified computationally by…

TIPR
Desktop

TIPR

A sequence-based machine learning model which identifies transcription start…

A sequence-based machine learning model which identifies transcription start sites (TSSs) with high accuracy and resolution for multiple spatial distribution patterns along the genome, including…

PROmiRNA
Desktop

PROmiRNA

A program for annotating miRNA promoters in human, as well as other species.…

A program for annotating miRNA promoters in human, as well as other species. PROmiRNA uses deepCAGE data from the FANTOM4 Consortium and integrated cage tag counts and other promoter features, such…

CoreBoost
Web

CoreBoost

A promoter prediction program which applies a boosting technique with stumps to…

A promoter prediction program which applies a boosting technique with stumps to select important small-scale as well as large-scale features. CoreBoost improves greatly on locating transcription…

Marina
Desktop

Marina

An open-source software tool for identifying over-represented transcription…

An open-source software tool for identifying over-represented transcription factors binding sites (TFBSs) from amongst large sets of promoter sequences, using an ensemble of 7 statistical metrics and…

MADAP
Desktop
Web

MADAP

Enables the user to customize the procedure to a specific problem. MADAP is a…

Enables the user to customize the procedure to a specific problem. MADAP is a flexible one-dimensional clustering tool for the inference of promoters from mRNA 5′ end profiles obtained from the…

PromFD
Desktop

PromFD

Identifies vertebrate RNA polymerase II promoters. PromFD determines a string…

Identifies vertebrate RNA polymerase II promoters. PromFD determines a string profile and a matrix profile of an input DNA sequence. It requires perfect matches of the input signals with a database…

TSRchitect
Desktop

TSRchitect

Identifies the putative promoter from a variety of TSS profiling data types,…

Identifies the putative promoter from a variety of TSS profiling data types, including both single-end as well as paired-end. TSRchitect can calculate the width, abundance and Shape Index, and…

BPROM
Web

BPROM

Predicts bacterial promoters. BPROM is based on a linear discriminant function…

Predicts bacterial promoters. BPROM is based on a linear discriminant function which combines characteristics describing functional motifs and oligonucleotide composition of these sites. It is able…

CORE
Dataset

CORE

Summarizes ElemeNT-predicted core promoter elements near CAGE and…

Summarizes ElemeNT-predicted core promoter elements near CAGE and RNA-seq-defined Drosophila melanogaster transcription start sites (TSSs). For each analyzed transcript, the existence of a putative…

ElemeNT
Web

ElemeNT Elements Navigation Tool

An interactive tool for rapid and convenient detection of core promoter…

An interactive tool for rapid and convenient detection of core promoter elements within a given sequence. The input sequence is searched against the position weight matrices (PWMs) of…

Twine
Desktop

Twine

A Java GUI with multiple graphical representations ('Views') of…

A Java GUI with multiple graphical representations ('Views') of enhancer alignments that displays motifs, as IUPAC consensus sequences or position frequency matrices, in the context of…

EvoPromoter
Desktop

EvoPromoter

A method for finding regulatory modules in Eukaryotic species using…

A method for finding regulatory modules in Eukaryotic species using phylogenetic data. The user inputs two files: alignment file for the sequences of interest, and the XML file of parameters and…

ProSOM
Desktop

ProSOM

A promoter prediction program based on unsupervised clustering of physical…

A promoter prediction program based on unsupervised clustering of physical properties of DNA. ProSOM can clearly distinguish between the structural profiles of promoter sequences and other genomic…

ARTS
Desktop

ARTS Accurate Recognition of Transcription Starts

A kernel based method that accurately recognizes transcription start sites in…

A kernel based method that accurately recognizes transcription start sites in human. The application of otherwise too computationally expensive support vector machines was made possible due to the…

Promoter
Web

Promoter

Predicts transcription start sites of vertebrate PolII promoters in DNA…

Predicts transcription start sites of vertebrate PolII promoters in DNA sequences. Promoter has been developed as an evolution of simulated transcription factors that interact with sequences in…

PromoterExplore…
Desktop

PromoterExplorer

Locate the positions of promoters. In this method, not only the local…

Locate the positions of promoters. In this method, not only the local distribution of pentamers, but also the positional CpG island features are considered. PromoterExplorer is tested based on…

APTE
Desktop

APTE

Locates potential A-form DNA promoter transcription elements in genomes. APTE…

Locates potential A-form DNA promoter transcription elements in genomes. APTE identifies blocks within a DNA sequence with negative A-DNA propensity energy that precede a specified promoter motif…

GPMiner
Web

GPMiner

A web application for identifying promoter regions and annotating regulatory…

A web application for identifying promoter regions and annotating regulatory features in user-input sequences. The GPMiner system has a gene group analysis function for analyzing the co-occurrence of…

D-Light on…
Desktop

D-Light on promoters

A client-server software package to store and query large amounts of…

A client-server software package to store and query large amounts of transcription factor binding sites (TFBS) data for any number of genomes. Users can add small-scale data to the server database…

TiProD
Dataset

TiProD

A database of human promoter sequences for which some functional features are…

A database of human promoter sequences for which some functional features are known. It allows a user to query individual promoters and the expression pattern they mediate, gene expression signatures…

TSSPlant
Desktop

TSSPlant

Predicts both TATA and TATA-less promoters in sequences of a wide spectrum of…

Predicts both TATA and TATA-less promoters in sequences of a wide spectrum of plant genomes. TSSPlant was developed by using large promoter collections from Plant Promoter Databases (ppdb) and…

iPro70-PseZNC
Web

iPro70-PseZNC

Identifies sigma70 promoters in prokaryote. iPro70-PseZNC is able to reflect…

Identifies sigma70 promoters in prokaryote. iPro70-PseZNC is able to reflect the common features of promoters in statistics. It is based on the multi-window Z-curve and pseudo oligonucleotide…

bTSSfinder
Web
Desktop

bTSSfinder bacterial Transcription Start Site finder

Predicts putative promoters for five classes of σ factors in Cyanobacteria (σ…

Predicts putative promoters for five classes of σ factors in Cyanobacteria (σ A, σ C, σ H, σ G and σ F) and for five classes of sigma factors in E. coli (σ 70, σ 38, σ 32, σ 28 and σ 24).…

iPro54-PseKNC
Web

iPro54-PseKNC

The sigma(54) promoters are unique in prokaryotic genome and responsible for…

The sigma(54) promoters are unique in prokaryotic genome and responsible for transcripting carbon and nitrogen-related genes. The web-server iPro54-PseKNC was developed to predict σ54 promoters in…

PromAn
Web

PromAn

Locates the promoter region on the reference genomic sequence and validates the…

Locates the promoter region on the reference genomic sequence and validates the transcription start site location. PromAn allows users to perform multiple alignment using more than two orthologous…

MCatch
Web

MCatch MatrixCatch

Identifies composite regulatory elements in promoters using a library of known…

Identifies composite regulatory elements in promoters using a library of known examples. MatrixCatch is a methodology that complements the lack of knowledge on sequence variation of each DNA binding…

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