Document Detail


Towards a resolution on the inherent methodological weakness of the "effective number of codons used by a gene".
MedLine Citation:
PMID:  15823544     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Recently Anders Fuglsang provided a modified way for calculating N(c) when biased discrepancy is present in a gene [Biochem. Biophys. Res. Commun. 317 (2004) 957]. Instead of taking the average codon homozygosity for each synonymous family type (as proposed by Wright) [Gene 87 (1990) 23] Fuglsang considered codon homozygosity of each amino acid individually. Marsashi and Najafabadi [Biochem. Biophys. Res. Commun. 324 (2004) 1] in their recent article demonstrated that the readjustment for overestimation at the level of individual amino acids results in loss of considerable amount of information. Immediately after the publication of Marsashi and Najafabadi, Fuglsang proposed that codon homozygosities can be calculated based on the classical population genetics [Biochem. Biophys. Res. Commun. 327 (2005) 1]. Though Fuglsang's approach is a novel one, it fails when any of the amino acids are absent in a gene. However, the inherent cause of overestimation at the level of individual amino acids is still obscured in the literature. Here in this communication we have presented a general condition where effective number of codons is overestimated using Wright's formula and also we propose a new way to calculate N(c), which is independent of amino acid composition.
Authors:
T Banerjee; S K Gupta; T C Ghosh
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Publication Detail:
Type:  Comment; Journal Article    
Journal Detail:
Title:  Biochemical and biophysical research communications     Volume:  330     ISSN:  0006-291X     ISO Abbreviation:  Biochem. Biophys. Res. Commun.     Publication Date:  2005 May 
Date Detail:
Created Date:  2005-04-12     Completed Date:  2005-07-05     Revised Date:  2006-11-15    
Medline Journal Info:
Nlm Unique ID:  0372516     Medline TA:  Biochem Biophys Res Commun     Country:  United States    
Other Details:
Languages:  eng     Pagination:  1015-8     Citation Subset:  IM    
Affiliation:
Bioinformatics Centre, Bose Institute, P 1/12, C.I.T. Scheme VII M, Kolkata 700 054, India.
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MeSH Terms
Descriptor/Qualifier:
Algorithms
Amidohydrolases / genetics
Amino Acids / genetics*
Codon*
Fusobacterium nucleatum / genetics
Homozygote*
Mycobacterium tuberculosis / genetics
Ribosomal Proteins / genetics
Chemical
Reg. No./Substance:
0/Amino Acids; 0/Codon; 0/Ribosomal Proteins; 70815-33-7/ribosomal protein L7-L12; EC 3.5.-/Amidohydrolases
Comments/Corrections
Comment On:
Biochem Biophys Res Commun. 2004 May 7;317(3):957-64   [PMID:  15081433 ]
Biochem Biophys Res Commun. 2005 Feb 4;327(1):1-3   [PMID:  15629420 ]

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