EP3 specifications


Unique identifier OMICS_24806
Name EP3
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Medium
Version 1.10
Stability Stable
Maintained Yes



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  • person_outline Yves Van de Peer <>

Additional information


Publication for EP3

EP3 in publications

PMCID: 5852095
PMID: 29540741
DOI: 10.1038/s41598-018-22129-8

[…] regions of tss. the results presented here suggested that prompredict can be potential algorithm for promoter prediction in eukaryotes. further, the performance of prompredict has been compared with ep3., the performance of prompredict has been compared with the other free energy based promoter predictor ep3 which has been applied primarily to predict mouse and human promoters (in the −1000 […]

PMCID: 3280155
PMID: 22226192
DOI: 10.1186/1471-2105-13-4

[…] vector machine, arts integrates several compositional features and two structural features. meanwhile, we include four newly proposed methods that depend on structural features to predict promoters. ep3 directly uses a deviation from the average structural value to locate the promoter regions []. observing the distinct structural patterns of promoter regions, pnnp develops a pattern-based […]

PMCID: 3053590
PMID: 21118509
DOI: 10.1186/1471-2164-11-677

[…] positives were counted, as variation in both will improve ensemble performance. predictions from only two pairs of programs overlapped by 50% or more. the highest overlap was between prosom [] and ep3 [], which are by the same authors and use the same features. firstef [], eponine [], and n-scan [] also had reasonable overlap between prediction sets. the average overlap between pairs […]

PMCID: 3009539
PMID: 20122241
DOI: 10.1186/1471-2105-11-S1-S65

[…] rank among the most discriminative variables from mean decrease in accuracy graph (figure )., we compared our algorithm with some of the existing best performing promoter prediction methods []: ep3 [], eponine [], firstef [], prosom 2.5 []. table and figure show that our classification model out-performs these existing programs based on independent (unseen) test set of pol-ii enriched […]

PMCID: 2794178
PMID: 19820114
DOI: 10.1093/nar/gkp821

[…] where region predictions were given, these were converted to appropriate point predictions. in addition, the pppbenchmark evaluation allowed us to compare performance versus a total of 17 methods., ep3 () is a promoter prediction program based on dinucleotide base-stacking energy. there is some correlation between base-stacking energy and melting temperature, but unlike our approach, ep3 […]

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EP3 institution(s)
Department of Plant Systems Biology, VIB, Ghent University, Gent, Belgium; Department of Plant Biotechnology and Genetics, Ghent University, Gent, Belgium
EP3 funding source(s)
Supported by the Institute for the Promotion of Innovation through Science and Technology in Flanders (IWT-Vlaanderen), and a Research Foundation Flanders (FWO-Vlaanderen) post-doctoral grant.

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