EpiMut: Alignment-independent tool for functional annotation of amino acid substitutions in epigenetic factors

Gemović, Branislava S.; Perović, Vladimir R.; Davidović, Radoslav S.; Veljković, Nevena

2019

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Software [ZIP] (14.17Mb)

EpiMut_Manual.pdf (127.5Kb)

Аутори

Gemović, Branislava S.

Perović, Vladimir R.

Davidović, Radoslav S.

Veljković, Nevena

Софтвер (Објављена верзија)

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Апстракт

EpiMut is software for functional annotation of AASs in epigenetic factors that is independent from sequence alignments and homology search. It is based on the biochemical and physicochemical characteristics of amino acids and digital signal processing approach in protein sequence analysis. EpiMut is a command line application that provides prediction scores for AASs in 19 epigenetic factors – ARID1A, ASXL1, ATM, ATRX, BCOR, CREBBP, DNMT3A, EP300, EZH2, JAK2, KMT2A, KMT2C, KMT2D, NSD1, SETD2, SF3B1, SPEN, TET2, TP53. It classifies AAS as neutral or disease-related. EpiMut models were generated for each gene separately and they represent Naïve Bayes classifiers trained on the EpiMut dataset (link). EpiMut is written in JAVA language and is available as standalone application, which can be executed on any operating system containing Java Virtual Machine. In order to run the EpiMut program it is necessary to install Java Runtime Environment 8 (JRE), which can be found for Windows, Linux,...

Извор:
VINČA Institute of Nuclear Sciences, University of Belgrade - Laboratory for Bioinformatics and Computational Chemistry, 2019

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Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
If using EpiMut, please cite: Gemovic B, Perovic V, Davidovic R and Veljkovic N. (2019) EpiMut: Alignment-independent tool for functional annotation of amino acid substitutions in epigenetic factors.
EpiMut application with documentation is provided at this URL: https://www.vin.bg.ac.rs/180/tools/epimut.php

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Институција/група

Vinča

TY - COMP
AU - Gemović, Branislava S.
AU - Perović, Vladimir R.
AU - Davidović, Radoslav S.
AU - Veljković, Nevena
PY - 2019
UR - https://vinar.vin.bg.ac.rs/handle/123456789/14200
AB - EpiMut is software for functional annotation of AASs in epigenetic factors that is independent from sequence alignments and homology search. It is based on the biochemical and physicochemical characteristics of amino acids and digital signal processing approach in protein sequence analysis. EpiMut is a command line application that provides prediction scores for AASs in 19 epigenetic factors – ARID1A, ASXL1, ATM, ATRX, BCOR, CREBBP, DNMT3A, EP300, EZH2, JAK2, KMT2A, KMT2C, KMT2D, NSD1, SETD2, SF3B1, SPEN, TET2, TP53. It classifies AAS as neutral or disease-related. EpiMut models were generated for each gene separately and they represent Naïve Bayes classifiers trained on the EpiMut dataset (link).
EpiMut is written in JAVA language and is available as standalone application, which can be executed on any operating system containing Java Virtual Machine. In order to run the EpiMut program it is necessary to install Java Runtime Environment 8 (JRE), which can be found for Windows, Linux, Mac OS and Solaris systems at: Java SE Runtime Environment 8 - Downloads.
T2 - VINČA Institute of Nuclear Sciences, University of Belgrade - Laboratory for Bioinformatics and Computational Chemistry
T1 - EpiMut: Alignment-independent tool for functional annotation of amino acid substitutions in epigenetic factors
UR - https://hdl.handle.net/21.15107/rcub_vinar_14200
ER -

@misc{
author = "Gemović, Branislava S. and Perović, Vladimir R. and Davidović, Radoslav S. and Veljković, Nevena",
year = "2019",
abstract = "EpiMut is software for functional annotation of AASs in epigenetic factors that is independent from sequence alignments and homology search. It is based on the biochemical and physicochemical characteristics of amino acids and digital signal processing approach in protein sequence analysis. EpiMut is a command line application that provides prediction scores for AASs in 19 epigenetic factors – ARID1A, ASXL1, ATM, ATRX, BCOR, CREBBP, DNMT3A, EP300, EZH2, JAK2, KMT2A, KMT2C, KMT2D, NSD1, SETD2, SF3B1, SPEN, TET2, TP53. It classifies AAS as neutral or disease-related. EpiMut models were generated for each gene separately and they represent Naïve Bayes classifiers trained on the EpiMut dataset (link).
EpiMut is written in JAVA language and is available as standalone application, which can be executed on any operating system containing Java Virtual Machine. In order to run the EpiMut program it is necessary to install Java Runtime Environment 8 (JRE), which can be found for Windows, Linux, Mac OS and Solaris systems at: Java SE Runtime Environment 8 - Downloads.",
journal = "VINČA Institute of Nuclear Sciences, University of Belgrade - Laboratory for Bioinformatics and Computational Chemistry",
title = "EpiMut: Alignment-independent tool for functional annotation of amino acid substitutions in epigenetic factors",
url = "https://hdl.handle.net/21.15107/rcub_vinar_14200"
}

Gemović, B. S., Perović, V. R., Davidović, R. S.,& Veljković, N.. (2019). EpiMut: Alignment-independent tool for functional annotation of amino acid substitutions in epigenetic factors. in VINČA Institute of Nuclear Sciences, University of Belgrade - Laboratory for Bioinformatics and Computational Chemistry.
https://hdl.handle.net/21.15107/rcub_vinar_14200

Gemović BS, Perović VR, Davidović RS, Veljković N. EpiMut: Alignment-independent tool for functional annotation of amino acid substitutions in epigenetic factors. in VINČA Institute of Nuclear Sciences, University of Belgrade - Laboratory for Bioinformatics and Computational Chemistry. 2019;.
https://hdl.handle.net/21.15107/rcub_vinar_14200 .

Gemović, Branislava S., Perović, Vladimir R., Davidović, Radoslav S., Veljković, Nevena, "EpiMut: Alignment-independent tool for functional annotation of amino acid substitutions in epigenetic factors" in VINČA Institute of Nuclear Sciences, University of Belgrade - Laboratory for Bioinformatics and Computational Chemistry (2019),
https://hdl.handle.net/21.15107/rcub_vinar_14200 .