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The gene-specific codon counting database

Citations: 8

z-index 0.00

Short name The gene-specific codon counting database
Full name The gene-specific codon counting database
Description a genome-based catalog of one-,two-,three-,four- and five-codon combinations present in Saccharomyces cerevisiae genes
URL http://www.cs.albany.edu/~tumu/GSCC.html
Year founded 2012
Last update & version 2012-02-08    V1.0
Availability Not Available
University/Institution hosted State University of New York Albany
Address Albany,NY 12222,USA
City Providence
Province/State NY
Country/Region United States
Contact name Thomas J. Begley
Contact email tbegley@uamail.albany.edu
Data type(s)
Major organism(s)
Keyword(s)
  • codon counting tool
  • multi-codon data
Publication(s)
  • The gene-specific codon counting database: a genome-based catalog of one-, two-, three-, four- and five-codon combinations present in Saccharomyces cerevisiae genes. [PMID: 22323063]

    Sudheer Tumu, Ashish Patil, William Towns, Madhu Dyavaiah, Thomas J Begley
    Database : the journal of biological databases and curation 2012:2012
    8 Citations (Google Scholar as of 2016-01-26)

    Abstract: A codon consists of three nucleotides and functions during translation to dictate the insertion of a specific amino acid in a growing peptide or, in the case of stop codons, to specify the completion of protein synthesis. There are 64 possible single codons and there are 4096 double, 262?144 triple, 16?777?216 quadruple and 1?073?741?824 quintuple codon combinations available for use by specific genes and genomes. In order to evaluate the use of specific single, double, triple, quadruple and quintuple codon combinations in genes and gene networks, we have developed a codon counting tool and employed it to analyze 5780 Saccharomyces cerevisiae genes. We have also developed visualization approaches, including codon painting, combination and bar graphs, and have used them to identify distinct codon usage patterns in specific genes and groups of genes. Using our developed Gene-Specific Codon Counting Database, we have identified extreme codon runs in specific genes. We have also demonstrated that specific codon combinations or usage patterns are over-represented in genes whose corresponding proteins belong to ribosome or translation-associated biological processes. Our resulting database provides a mineable list of multi-codon data and can be used to identify unique sequence runs and codon usage patterns in individual and functionally linked groups of genes.

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Tags

DNA
Saccharomyces cerevisiae
codon counting tool multi-codon data

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Zhang Zhang [2016-04-26]
    • Guangyu Wang [2016-04-01]
    • Guangyu Wang [2015-12-06]
    • Guangyu Wang [2015-06-26]
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