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Codon and Codon-Pair Usage Tables (CoCoPUTs): Facilitating Genetic Variation Analyses and Recombinant Gene Design.
Alexaki, Aikaterini; Kames, Jacob; Holcomb, David D; Athey, John; Santana-Quintero, Luis V; Lam, Phuc Vihn Nguyen; Hamasaki-Katagiri, Nobuko; Osipova, Ekaterina; Simonyan, Vahan; Bar, Haim; Komar, Anton A; Kimchi-Sarfaty, Chava.
Afiliación
  • 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.
  • 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.
  • 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.
  • 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.
  • Santana-Quintero LV; High Performance Integrated Environment, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA.
  • Lam PVN; High Performance Integrated Environment, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA.
  • 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.
  • Osipova E; High Performance Integrated Environment, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA.
  • Simonyan V; High Performance Integrated Environment, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA.
  • Bar H; Department of Statistics, University of Connecticut, Storrs, CT 06268, USA.
  • Komar AA; Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH 44115, USA. Electronic address: a.komar@csuohio.edu.
  • 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.
J Mol Biol ; 431(13): 2434-2441, 2019 06 14.
Article en En | MEDLINE | ID: mdl-31029701
ABSTRACT
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.
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Texto completo: 1 Bases de datos: MEDLINE Asunto principal: Variación Genética / Biología Computacional / Uso de Codones Límite: Humans Idioma: En Revista: J Mol Biol Año: 2019 Tipo del documento: Article País de afiliación: Estados Unidos
Texto completo
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Bases de datos: MEDLINE Asunto principal: Variación Genética / Biología Computacional / Uso de Codones Límite: Humans Idioma: En Revista: J Mol Biol Año: 2019 Tipo del documento: Article País de afiliación: Estados Unidos