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Bigram-PGK: phosphoglycerylation prediction using the technique of bigram probabilities of position specific scoring matrix
BACKGROUND: The biological process known as post-translational modification (PTM) is a condition whereby proteomes are modified that affects normal cell biology, and hence the pathogenesis. A number of PTMs have been discovered in the recent years and lysine phosphoglycerylation is one of the fairly...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6923822/ https://www.ncbi.nlm.nih.gov/pubmed/31856704 http://dx.doi.org/10.1186/s12860-019-0240-1 |
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author | Chandra, Abel Sharma, Alok Dehzangi, Abdollah Shigemizu, Daichi Tsunoda, Tatsuhiko |
author_facet | Chandra, Abel Sharma, Alok Dehzangi, Abdollah Shigemizu, Daichi Tsunoda, Tatsuhiko |
author_sort | Chandra, Abel |
collection | PubMed |
description | BACKGROUND: The biological process known as post-translational modification (PTM) is a condition whereby proteomes are modified that affects normal cell biology, and hence the pathogenesis. A number of PTMs have been discovered in the recent years and lysine phosphoglycerylation is one of the fairly recent developments. Even with a large number of proteins being sequenced in the post-genomic era, the identification of phosphoglycerylation remains a big challenge due to factors such as cost, time consumption and inefficiency involved in the experimental efforts. To overcome this issue, computational techniques have emerged to accurately identify phosphoglycerylated lysine residues. However, the computational techniques proposed so far hold limitations to correctly predict this covalent modification. RESULTS: We propose a new predictor in this paper called Bigram-PGK which uses evolutionary information of amino acids to try and predict phosphoglycerylated sites. The benchmark dataset which contains experimentally labelled sites is employed for this purpose and profile bigram occurrences is calculated from position specific scoring matrices of amino acids in the protein sequences. The statistical measures of this work, such as sensitivity, specificity, precision, accuracy, Mathews correlation coefficient and area under ROC curve have been reported to be 0.9642, 0.8973, 0.8253, 0.9193, 0.8330, 0.9306, respectively. CONCLUSIONS: The proposed predictor, based on the feature of evolutionary information and support vector machine classifier, has shown great potential to effectively predict phosphoglycerylated and non-phosphoglycerylated lysine residues when compared against the existing predictors. The data and software of this work can be acquired from https://github.com/abelavit/Bigram-PGK. |
format | Online Article Text |
id | pubmed-6923822 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-69238222019-12-30 Bigram-PGK: phosphoglycerylation prediction using the technique of bigram probabilities of position specific scoring matrix Chandra, Abel Sharma, Alok Dehzangi, Abdollah Shigemizu, Daichi Tsunoda, Tatsuhiko BMC Mol Cell Biol Research BACKGROUND: The biological process known as post-translational modification (PTM) is a condition whereby proteomes are modified that affects normal cell biology, and hence the pathogenesis. A number of PTMs have been discovered in the recent years and lysine phosphoglycerylation is one of the fairly recent developments. Even with a large number of proteins being sequenced in the post-genomic era, the identification of phosphoglycerylation remains a big challenge due to factors such as cost, time consumption and inefficiency involved in the experimental efforts. To overcome this issue, computational techniques have emerged to accurately identify phosphoglycerylated lysine residues. However, the computational techniques proposed so far hold limitations to correctly predict this covalent modification. RESULTS: We propose a new predictor in this paper called Bigram-PGK which uses evolutionary information of amino acids to try and predict phosphoglycerylated sites. The benchmark dataset which contains experimentally labelled sites is employed for this purpose and profile bigram occurrences is calculated from position specific scoring matrices of amino acids in the protein sequences. The statistical measures of this work, such as sensitivity, specificity, precision, accuracy, Mathews correlation coefficient and area under ROC curve have been reported to be 0.9642, 0.8973, 0.8253, 0.9193, 0.8330, 0.9306, respectively. CONCLUSIONS: The proposed predictor, based on the feature of evolutionary information and support vector machine classifier, has shown great potential to effectively predict phosphoglycerylated and non-phosphoglycerylated lysine residues when compared against the existing predictors. The data and software of this work can be acquired from https://github.com/abelavit/Bigram-PGK. BioMed Central 2019-12-20 /pmc/articles/PMC6923822/ /pubmed/31856704 http://dx.doi.org/10.1186/s12860-019-0240-1 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Chandra, Abel Sharma, Alok Dehzangi, Abdollah Shigemizu, Daichi Tsunoda, Tatsuhiko Bigram-PGK: phosphoglycerylation prediction using the technique of bigram probabilities of position specific scoring matrix |
title | Bigram-PGK: phosphoglycerylation prediction using the technique of bigram probabilities of position specific scoring matrix |
title_full | Bigram-PGK: phosphoglycerylation prediction using the technique of bigram probabilities of position specific scoring matrix |
title_fullStr | Bigram-PGK: phosphoglycerylation prediction using the technique of bigram probabilities of position specific scoring matrix |
title_full_unstemmed | Bigram-PGK: phosphoglycerylation prediction using the technique of bigram probabilities of position specific scoring matrix |
title_short | Bigram-PGK: phosphoglycerylation prediction using the technique of bigram probabilities of position specific scoring matrix |
title_sort | bigram-pgk: phosphoglycerylation prediction using the technique of bigram probabilities of position specific scoring matrix |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6923822/ https://www.ncbi.nlm.nih.gov/pubmed/31856704 http://dx.doi.org/10.1186/s12860-019-0240-1 |
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