EPIP – Condition-specific Enhancer–promoter Interaction prediction

EPIP

:: DESCRIPTION

EPIP is a software used to identify target genes of enhancers in human genome. It is a novel computational method to reliably predict EPIs, especially condition-specific ones. EPIP is capable of predicting interactions in samples with limited data as well as in samples with abundant data.

::DEVELOPER

Hu Lab – Data Integration and Knowledge Discovery @ UCF

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Python

:: DOWNLOAD

EPIP

:: MORE INFORMATION

Citation:

Bioinformatics. 2019 Oct 15;35(20):3877-3883. doi: 10.1093/bioinformatics/btz641.
EPIP: a novel approach for condition-specific enhancer-promoter interaction prediction.
Talukder A, Saadat S, Li X, Hu H.

PEP – Predict Enhancer Promoter interactions

PEP

:: DESCRIPTION

PEP is a framework for predicting long-range enhancer-promoter interactions (EPI) incorporating two strategies for extracting features directly from the DNA sequences of enhancer and promoter elements

::DEVELOPER

Ma Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

PEP

:: MORE INFORMATION

Citation

Exploiting sequence-based features for predicting enhancer-promoter interactions.
Yang Y, Zhang R, Singh S, Ma J.
Bioinformatics. 2017 Jul 15;33(14):i252-i260. doi: 10.1093/bioinformatics/btx257

ElemeNT – Tool for Detection of core Promoter Elements

ElemeNT

:: DESCRIPTION

ElemeNT (Elements Navigation Tool) is an interactive tool for rapid and convenient detection of core promoter elements within a given sequence, implemented in Perl programming language.

::DEVELOPER

Juven-Gershon Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Transcription. 2015;6(3):41-50. doi: 10.1080/21541264.2015.1067286.
ElemeNT: a computational tool for detecting core promoter elements.
Sloutskin A, Danino YM, Orenstein Y, Zehavi Y, Doniger T, Shamir R, Juven-Gershon T.

PrimerZ 20171130 – Streamlined Primer design for Promoters, Exons and Human SNPs

PrimerZ 20171130

:: DESCRIPTION

PrimerZ is a web application dedicated primarily to primer design for genes and human SNPs.

::DEVELOPER

PrimerZ team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PrimerZ: streamlined primer design for promoters, exons and human SNPs.
Tsai MF, Lin YJ, Cheng YC, Lee KH, Huang CC, Chen YT, Yao A.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W63-5. Epub 2007 May 30.

CpGProD – Predict Mammalian Promoters Associated with CpG Islands

CpGProD

:: DESCRIPTION

CpGProD (CpG Island Promoter Detection) is an application for identifying mammalian promoter regions associated with CpG islands in large genomic sequences. Although it is strictly dedicated to this particular promoter class corresponding to ≈50% of the genes, CpGProD exhibits a higher sensitivity and specificity than other tools used for promoter prediction. Notably, CpGProD uses different parameters according to species (human, mouse) studied. Moreover, CpGProD predicts the promoter orientation on the DNA strand.

CpGProD Online Version

::DEVELOPER

PRABI-Doua

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  Mac OsX / Linux

:: DOWNLOAD

 CpGProD

:: MORE INFORMATION

Citation

Ponger, L. and Mouchiroud, D. (2001)
CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequences.
Bioinformatics, 18, 631-633

iProEP – Predictor for Predicting Promoter

iProEP

:: DESCRIPTION

iProEP is a promoter prediction tools of five species: Homo sapiens, Drosophila melanogaster, Caenorhabditis elegans, Bacillus subtilis, and Escherichia coli. The PseKNC and PCSF features were employed to formulate promoter samples.

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

iProEP: A Computational Predictor for Predicting Promoter.
Lai HY, Zhang ZY, Su ZD, Su W, Ding H, Chen W, Lin H.
Mol Ther Nucleic Acids. 2019 Sep 6;17:337-346. doi: 10.1016/j.omtn.2019.05.028.

iPro54-PseKNC – Predicting Promoters with Pseudo k-tuple Nucleotide Composition

iPro54-PseKNC

:: DESCRIPTION

iPro54-PseKNC is a sequence-based predictor for identifying σ54 promoters with pseudo k-tuple nucleotide composition

::DEVELOPER

LinDing Group

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition.
Lin H, Deng EZ, Ding H, Chen W, Chou KC.
Nucleic Acids Res. 2014 Dec 1;42(21):12961-72. doi: 10.1093/nar/gku1019

SigmaPromoter 1.0 – Promoter Prediction method based on multiple Sigma Factors model for Bacterial Genomes

SigmaPromoter 1.0

:: DESCRIPTION

SigmaPromoter is a method of providing predictions for four chosen sigma promoters as an attempt to comprehensively characterize and predict non-housekeeping sigma promoters.

::DEVELOPER

ZhuLab, Peking Uiniversity, Beijing

 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows

:: DOWNLOAD

 SigmaPromoter

:: MORE INFORMATION

MatrixCatch 2.7 – Recognition of Composite Regulatory Elements in Promoters

MatrixCatch 2.7

:: DESCRIPTION

MatrixCatch (MCatch) is a tool designed to search for potential composite elements (CEs) in DNA sequences.

::DEVELOPER

MatrixCatch team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Aug 8;14:241. doi: 10.1186/1471-2105-14-241.
MatrixCatch–a novel tool for the recognition of composite regulatory elements in promoters.
Deyneko IV, Kel AE, Kel-Margoulis OV, Deineko EV, Wingender E, Weiss S.

HIPPIE 0.0.2b – High-Throughput Identification Pipeline for Promoter Interacting Enhancer elements

HIPPIE 0.0.2b

:: DESCRIPTION

HIPPIE is the workflow for analyzing Hi-C paired-end reads in FASTQ format and predict enhancer–target gene interactions. HIPPIE streamlines the entire processing phase including reads mapping, quality control and enhancer–target gene prediction as well as characterizing the interactions.

::DEVELOPER

Wang Lab @ IBI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 HIPPIE

:: MORE INFORMATION

Citation

HIPPIE: A high-throughput identification pipeline for promoter interacting enhancer elements.
Hwang YC, Lin CF, Valladares O, Malamon J, Kuksa P, Zheng Q, Gregory BD, Wang LS.
Bioinformatics. 2014 Dec 4. pii: btu801.