Full Length Research Paper
References
|
Angellotti MC, Bhuiyan SB, Chen G, Wan X (2007). CodonO: codon usage bias analysis within and across genomes. Nucleic Acids Res. 35:W132-W136. Crossref |
||||
|
Bernardi G, Mouchiroud D, Gautier C (1993). Silent substitutions in mammalian genomes and their evolutionary implications. J. Mol. Evol. 37:583-589. Crossref |
||||
|
Chen SL, Lee W, Hottes AK, Shapiro L, McAdams HH (2004). Codon usage between genomes is constrained by genome-wide mutational processes. Proc. Natl. Acad. Sci. USA 101:3480-3485. Crossref |
||||
|
Deschavanne I, Filipski J (1995). Correlation of GC content with replication timing and repair mechanisms in weakly expressed E. co/i genes. Nucleic Acids Res. 23:1350-1353. Crossref |
||||
|
D'Onofrio G, Bernardi G (1992). A universal compositional correlation among codon positions. Gene 110(1):81-8. Crossref |
||||
|
Duret L (2002).Evolution of synonymous codon usage in metazoans. Curr. Opin. Genet. Dev. 12:640-649. Crossref |
||||
|
Ermolaeva MD (2001). Synonymous codon usage in bacteria. Curr. Iss. Mol. Biol. 3:91-97. Pubmed |
||||
|
Grantham R, Gautier C, Gouy M, Jacobzone M, Mercier R (1981). Codon catalog usage is a genome strategy modulated for gene expressivity. Nucleic Acids Res. 9:43-74. Crossref |
||||
| Hammer Ø, Harper DAT, Ryan PD (2001). PAST: Paleontological Statistics Software Package for Education and Data Analysis. Palaeontologia Electronica 4(1):9. | ||||
| Henry I (2007). Evolution of Codon Usage in Bacteria. Ph.D thesis. University of Nottingham.U.K. | ||||
|
Ikemura T (1985). Codon usage and tRNA content in unicellular and multicellular organisms. Mol. Biol. Evol. 2:13-34. Pubmed |
||||
|
Kanaya S, Yamada Y, Kudo Y, Ikemura T (1999). Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis. Gene 238:143-155. Crossref |
||||
|
Karlin S, Campbell AM, Mrázek J (1998). Comparative DNA analysis across diverse genomes. Annu. Rev. Genet. 32:185-225. Crossref |
||||
|
Levin DB, Whittome B (2000). Codon usage in nucleopolyhedroviruses. J. Gen. Virol. 81:2313-2325. Pubmed |
||||
|
McInerney JO (1997). Prokaryotic genome evolution as assessed by multivariate analysis of codon usage patterns. Microb. Compar. Genomics 2(1):1-10. Crossref |
||||
|
McInerney JO (1998). Replicational and transcriptional selection on codon usage in Borrelia burgdorferi. Proc. Natl. Acad. Sci. USA 95: 10698-10703 Crossref |
||||
|
Nichols BP, Miozzari GF, Cleemput MV, Bennet GN, Yanofsky C (1980). Nucleotide sequences of the trpG regions of Escherichia coli, Shigella dysenteriae, Salmonella typhimurium and Serratia marcescens. J. Mol. Biol. 142:503-517. Crossref |
||||
|
O'Neil PK, Or M, Erill I (2013). scnRCA: A Novel Method to Detect Consistent Patterns of Translational Selection in Mutationally-Biased Genomes. PLoS ONE 8(10):e76177. Crossref |
||||
| Peden JF (1999). Analysis of Codon Usage, Ph.D. Thesis, University of Nottingham. | ||||
|
Prabha R, Singh DP, Gupta SK, Farooqi S, Rai A (2012). Synonymous codon usage in Thermosynechococcus elongatus (cyanobacteria) identifies the factors shaping codon usage variation. Bioinformation 8(13):622-628. Crossref |
||||
|
Puigbo P, Bravo IG, Garcia-Vallve S (2008) CAIcal: a combined set of tools to assess codon usage adaptation. Biol. Direct 3(1):38. Crossref |
||||
|
Seffernick JL, Erickson JS, Cameron SM, Cho S, Dodge AG, Richman JE, Sadowsky MJ, Wackett LP (2012). Defining Sequence Space and Reaction Products within the Cyanuric Acid Hydrolase (AtzD)/Barbiturase Protein Family. J. Bacterial. 194(17):4579 - 4588. Crossref |
||||
|
Sharp PM, Li WH (1987). The codon adaptation index—a measure of directional synonymous codon usage bias and its potential applications. Nucleic Acids Res. 15:1281-1295. Crossref |
||||
|
Sharp PM, Matassi G (1994). Codon usage and genome evolution. Curr. Opin. Genet. Dev. 4 (6):851-860. Crossref |
||||
|
Soong CL, Ogawa J, Sakuradani E, Shimizu S (2002). Barbiturase, a novel zinc-containing amidohydrolase involved in oxidative pyrimidine metabolism. J. Biol. Chem. 277:7051-7058. Crossref |
||||
|
Soong CL, Ogawa J, Shimizu S (2001). Novel amidohydrolytic reactions in oxidative pyrimidine metabolism: analysis of the barbiturase reaction and discovery of a novel enzyme, ureidomalonase. Biochem. Biophys. Res. Commun. 286:222-226 Crossref |
||||
|
Sueoka N (1988). Directional mutation pressure and neutral molecular evolution. Proc. Natl. Acad. Sci. USA 85(8): 2653-2657. Crossref |
||||
|
Sueoka N (1992). Directional mutation pressure, selective constraints and genetic equilibria. J. Mol. Evol. 34:95-114 Crossref |
||||
|
Tamura K, Nei M (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10:512-526. Pubmed |
||||
|
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011). MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol. Biol. Evol. 28:2731-2739. Crossref |
||||
|
Wan XF, Zhou J, Xu D (2006). CodonO: a new informatics method measuring synonymous codon usage bias. Int. J. Gen.Sys. 35:109-125. Crossref |
||||
|
Wolfe KH, Sharp PM, Li WH (1989). Mutation rates differ among regions of the mammalian genome. Nature 337:283-285. Crossref |
||||
|
Wright F (1990).The effective number of codons used in a gene. Gene 87(1):23-29 Crossref |
||||
Copyright © 2024 Author(s) retain the copyright of this article.
This article is published under the terms of the Creative Commons Attribution License 4.0
