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Integration of Residue Attributes for Sequence Diversity Characterization of Terpenoid Enzymes

Progress in the “omics” fields such as genomics, transcriptomics, proteomics, and metabolomics has engendered a need for innovative analytical techniques to derive meaningful information from the ever increasing molecular data. KNApSAcK motorcycle DB is a popular database for enzymes related to seco...

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Autores principales: Kibinge, Nelson, Ikeda, Shun, Ono, Naoaki, Altaf-Ul-Amin, Md., Kanaya, Shigehiko
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi Publishing Corporation 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034505/
https://www.ncbi.nlm.nih.gov/pubmed/24900985
http://dx.doi.org/10.1155/2014/753428
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author Kibinge, Nelson
Ikeda, Shun
Ono, Naoaki
Altaf-Ul-Amin, Md.
Kanaya, Shigehiko
author_facet Kibinge, Nelson
Ikeda, Shun
Ono, Naoaki
Altaf-Ul-Amin, Md.
Kanaya, Shigehiko
author_sort Kibinge, Nelson
collection PubMed
description Progress in the “omics” fields such as genomics, transcriptomics, proteomics, and metabolomics has engendered a need for innovative analytical techniques to derive meaningful information from the ever increasing molecular data. KNApSAcK motorcycle DB is a popular database for enzymes related to secondary metabolic pathways in plants. One of the challenges in analyses of protein sequence data in such repositories is the standard notation of sequences as strings of alphabetical characters. This has created lack of a natural underlying metric that eases amenability to computation. In view of this requirement, we applied novel integration of selected biochemical and physical attributes of amino acids derived from the amino acid index and quantified in numerical scale, to examine diversity of peptide sequences of terpenoid synthases accumulated in KNApSAcK motorcycle DB. We initially generated a reduced amino acid index table. This is a set of biochemical and physical properties obtained by random forest feature selection of important indices from the amino acid index. Principal component analysis was then applied for characterization of enzymes involved in synthesis of terpenoids. The variance explained was increased by incorporation of residue attributes for analyses.
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spelling pubmed-40345052014-06-04 Integration of Residue Attributes for Sequence Diversity Characterization of Terpenoid Enzymes Kibinge, Nelson Ikeda, Shun Ono, Naoaki Altaf-Ul-Amin, Md. Kanaya, Shigehiko Biomed Res Int Research Article Progress in the “omics” fields such as genomics, transcriptomics, proteomics, and metabolomics has engendered a need for innovative analytical techniques to derive meaningful information from the ever increasing molecular data. KNApSAcK motorcycle DB is a popular database for enzymes related to secondary metabolic pathways in plants. One of the challenges in analyses of protein sequence data in such repositories is the standard notation of sequences as strings of alphabetical characters. This has created lack of a natural underlying metric that eases amenability to computation. In view of this requirement, we applied novel integration of selected biochemical and physical attributes of amino acids derived from the amino acid index and quantified in numerical scale, to examine diversity of peptide sequences of terpenoid synthases accumulated in KNApSAcK motorcycle DB. We initially generated a reduced amino acid index table. This is a set of biochemical and physical properties obtained by random forest feature selection of important indices from the amino acid index. Principal component analysis was then applied for characterization of enzymes involved in synthesis of terpenoids. The variance explained was increased by incorporation of residue attributes for analyses. Hindawi Publishing Corporation 2014 2014-05-11 /pmc/articles/PMC4034505/ /pubmed/24900985 http://dx.doi.org/10.1155/2014/753428 Text en Copyright © 2014 Nelson Kibinge et al. https://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Kibinge, Nelson
Ikeda, Shun
Ono, Naoaki
Altaf-Ul-Amin, Md.
Kanaya, Shigehiko
Integration of Residue Attributes for Sequence Diversity Characterization of Terpenoid Enzymes
title Integration of Residue Attributes for Sequence Diversity Characterization of Terpenoid Enzymes
title_full Integration of Residue Attributes for Sequence Diversity Characterization of Terpenoid Enzymes
title_fullStr Integration of Residue Attributes for Sequence Diversity Characterization of Terpenoid Enzymes
title_full_unstemmed Integration of Residue Attributes for Sequence Diversity Characterization of Terpenoid Enzymes
title_short Integration of Residue Attributes for Sequence Diversity Characterization of Terpenoid Enzymes
title_sort integration of residue attributes for sequence diversity characterization of terpenoid enzymes
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034505/
https://www.ncbi.nlm.nih.gov/pubmed/24900985
http://dx.doi.org/10.1155/2014/753428
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