:: DESCRIPTION
Sunflower is an evolutionary model for promoters, analogous to the commonly used synonymous/nonsynonymous mutation models for protein-coding sequences.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Hoffman MM, Birney E. 2010.
An effective model for natural selection in promoters.
Genome Res. 20(5):685-692.
:: DESCRIPTION
TSRchitect allows the user to efficiently identify the putative promoter (the transcription start region, or TSR) from a variety of TSS profiling data types, including both single-end (e.g. CAGE) as well as paired-end (RAMPAGE, PEAT, STRIPE-seq).
::DEVELOPER
The Brendel Group @ Indiana University
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Raborn RT, Brendel VP.
Using RAMPAGE to Identify and Annotate Promoters in Insect Genomes.
Methods Mol Biol. 2019;1858:99-116. doi: 10.1007/978-1-4939-8775-7_9. PMID: 30414114.
:: DESCRIPTION
GoRAMPAGE is a workflow for promoter detection by 5′-read mapping.
::DEVELOPER
The Brendel Group @ Indiana University
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Raborn RT, Brendel VP.
Using RAMPAGE to Identify and Annotate Promoters in Insect Genomes.
Methods Mol Biol. 2019;1858:99-116. doi: 10.1007/978-1-4939-8775-7_9. PMID: 30414114.
:: 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
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: 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.
:: DESCRIPTION
PROmiRNA is a new approach for miRNA promoter annotation based on a semi-supervised statistical model trained on deepCAGE data and sequence features.
::DEVELOPER
PROmiRNA team , Max Planck Institute for Molecular Genetics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Genome Biol. 2013 Aug 16;14(8):R84. [Epub ahead of print]
PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs.
Marsico A1, Huska MR, Lasserre J, Hu H, Vucicevic D, Musahl A, Orom UA, Vingron M.
:: DESCRIPTION
iPromoter-2L is a predictor for identifying promoters and their types by combining Smoothing Cutting Window algorithm and sequence-based features
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Liu B, Li K.
iPromoter-2L2.0: Identifying Promoters and Their Types by Combining Smoothing Cutting Window Algorithm and Sequence-Based Features.
Mol Ther Nucleic Acids. 2019 Dec 6;18:80-87. doi: 10.1016/j.omtn.2019.08.008. Epub 2019 Aug 14. PMID: 31536883; PMCID: PMC6796744.
Liu B, Yang F, Huang DS, Chou KC.
iPromoter-2L: a two-layer predictor for identifying promoters and their types by multi-window-based PseKNC.
Bioinformatics. 2018 Jan 1;34(1):33-40. doi: 10.1093/bioinformatics/btx579. PMID: 28968797.
:: DESCRIPTION
RIPPLE is a software tool to predict enhancer-promoter interactions. RIPPLE is based random forests classification that trains a binary classifier for interactions inferred from Hi-C or 5C data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Roy S, Siahpirani AF, Chasman D, Knaack S, Ay F, Stewart R, Wilson M, Sridharan R.
A predictive modeling approach for cell line-specific long-range regulatory interactions.
Nucleic Acids Res. 2015 Oct 15;43(18):8694-712. doi: 10.1093/nar/gkv865. Epub 2015 Sep 3. Erratum in: Nucleic Acids Res. 2016 Feb 29;44(4):1977-8. PMID: 26338778; PMCID: PMC4605315.
:: DESCRIPTION
Graphviz is a powerful open-source tool that visualizes graphs and networks.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
MatrixCatch (MCatch) is a tool designed to search for potential composite elements (CEs) in DNA sequences.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: 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.
:: DESCRIPTION
MotifIndexer is a comprehensive strategy for de novo identification of DNA regulatory motifs at a genome level.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Ma S, Bachan S, Porto M, Bohnert HJ, Snyder M and Dinesh-Kumar SP. (2012)
Discovery of stress responsive DNA regulatory motifs in Arabidopsis.
PLoS ONE 7:e43198
