Codon and Codon-Pair Usage Tables (CoCoPUTs): Facilitating Genetic Variation Analyses and Recombinant Gene Design.

Algorithms Base Sequence Codon Usage Computational Biology / methods Databases, Genetic Genetic Variation Humans
GenBank codon context codon-pair bias dinucleotide frequency gene optimization/deoptimization

Journal

Journal of molecular biology
ISSN: 1089-8638
Titre abrégé: J Mol Biol
Pays: Netherlands
ID NLM: 2985088R

Informations de publication

Date de publication:
14 06 2019
Historique:
received: 01 02 2019
revised: 10 04 2019
accepted: 15 04 2019
pubmed: 29 4 2019
medline: 6 6 2020
entrez: 29 4 2019
Statut: ppublish

Résumé

Usage of sequential codon-pairs is non-random and unique to each species. Codon-pair bias is related to but clearly distinct from individual codon usage bias. Codon-pair bias is thought to affect translational fidelity and efficiency and is presumed to be under the selective pressure. It was suggested that changes in codon-pair utilization may affect human disease more significantly than changes in single codons. Although recombinant gene technologies often take codon-pair usage bias into account, codon-pair usage data/tables are not readily available, thus potentially impeding research efforts. The present computational resource (https://hive.biochemistry.gwu.edu/review/codon2) systematically addresses this issue. Building on our recent HIVE-Codon Usage Tables, we constructed a new database to include genomic codon-pair and dinucleotide statistics of all organisms with sequenced genome, available in the GenBank. We believe that the growing understanding of the importance of codon-pair usage will make this resource an invaluable tool to many researchers in academia and pharmaceutical industry.

Identifiants

DOI: 10.1016/j.jmb.2019.04.021 PMID: 31029701
pubmed: 31029701
pii: S0022-2836(19)30228-1
doi: 10.1016/j.jmb.2019.04.021
pii:
doi:

Types de publication

Journal Article Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

Langues

eng

Sous-ensembles de citation

IM

Pagination

2434-2441

Informations de copyright

Published by Elsevier Ltd.

Auteurs

Aikaterini Alexaki (A)

Division of Plasma Protein Therapeutics, Office of Tissue and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA.

Jacob Kames (J)

Division of Plasma Protein Therapeutics, Office of Tissue and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA.

David D Holcomb (DD)

Division of Plasma Protein Therapeutics, Office of Tissue and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA.

John Athey (J)

Division of Plasma Protein Therapeutics, Office of Tissue and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA.

Luis V Santana-Quintero (LV)

High Performance Integrated Environment, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA.

Phuc Vihn Nguyen Lam (PVN)

High Performance Integrated Environment, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA.

Nobuko Hamasaki-Katagiri (N)

Division of Plasma Protein Therapeutics, Office of Tissue and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA.

Ekaterina Osipova (E)

High Performance Integrated Environment, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA.

Vahan Simonyan (V)

High Performance Integrated Environment, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA.

Haim Bar (H)

Department of Statistics, University of Connecticut, Storrs, CT 06268, USA.

Anton A Komar (AA)

Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH 44115, USA. Electronic address: a.komar@csuohio.edu.

Chava Kimchi-Sarfaty (C)

Division of Plasma Protein Therapeutics, Office of Tissue and Advanced Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA. Electronic address: Chava.kimchi-sarfaty@fda.hhs.gov.

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Classifications MeSH

questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Algorithmes › Codon and Codon-Pair Usage Tables (CoCoPUTs):...
questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Données de séquences moléculaires › Séquence nucléotidique › Codon and Codon-Pair Usage Tables (CoCoPUTs):...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Code génétique › Usage des codons › Codon and Codon-Pair Usage Tables (CoCoPUTs):...
questionsmedicales.fr › Sciences de l'information › Informatique › Biologie informatique › Codon and Codon-Pair Usage Tables (CoCoPUTs):...
questionsmedicales.fr › Sciences de l'information › Mémorisation et recherche des informations › Bases de données comme sujet › Bases de données factuelles › Bases de données génétiques › Codon and Codon-Pair Usage Tables (CoCoPUTs):...
questionsmedicales.fr › Phénomènes génétiques › Variation génétique › Codon and Codon-Pair Usage Tables (CoCoPUTs):...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Codon and Codon-Pair Usage Tables (CoCoPUTs):...