Results 51 to 60 of about 9,001 (100)

A codon model of nucleotide substitution with selection on synonymous codon usage [PDF]

Molecular Phylogenetics and Evolution, 2014
ABSTRACTThe quality of phylogenetic inference made from protein-coding genes depends, in part, on the realism with which the codon substitution process is modeled. Here we propose a new mechanistic model that combines the standard M0 substitution model of Yang (1997) with a simplified model from Gilchrist (2007) that includes selection on synonymous ...
Kubatko, Laura, Shah, Premal, Herbei, Radu, Gilchrist, Michael   +3 more
openaire   +4 more sources

Comparative Study on Codon Usage Patterns across Chloroplast Genomes of Eighteen Taraxacum Species

Horticulturae
This study investigates codon usage bias within the chloroplast genomes of 18 Taraxacum species, focusing on the base composition and various metrics including GC content, Relative Synonymous Codon Usage (RSCU), Effective Number of Codons (ENc), and GC3s.
Yang Yang, Xingliang Wang, Zhenjie Shi
doaj   +1 more source

Antigenic and immunogenic properties of the canine distemper virus nucleocapsid protein expressed in Escherichia coli employing codon optimized synthetic gene

Pesquisa Veterinária Brasileira
: Despite common occurrence and importance of canine distemper disease the majority of tests currently available for diagnosis are hampered by either low sensitivity or specificity. In this study it was evaluated antigenic and immunogenic characteristics
Maureen H.V. Fernandes, Paula F. Finger, Rodrigo C. Cunha, Gilberto D’Avila Vargas, Geferson Fischer, Marcelo de Lima, Silvia O. Hübner   +6 more
doaj   +1 more source

Codon usage in nucleopolyhedroviruses

Journal of General Virology, 2000
Phylogenetic analyses based on baculovirus polyhedrin nucleotide and amino acid sequences revealed two major nucleopolyhedrovirus (NPV) clades, designated Group I and Group II. Subsequent phylogenetic analyses have revealed three Group II subclades, designated A, B and C.
Beatrixe Whittome, David B. Levin
openaire   +2 more sources

The Involvement of YNR069C in Protein Synthesis in the Baker’s Yeast, Saccharomyces cerevisiae

Biology
Maintaining translation fidelity is a critical step within the process of gene expression. It requires the involvement of numerous regulatory elements to ensure the synthesis of functional proteins. The efficient termination of protein synthesis can play
Sarah Takallou, Maryam Hajikarimlou, Mustafa Al-gafari, Jiashu Wang, Thomas David Daniel Kazmirchuk, Kamaledin B. Said, Bahram Samanfar, Ashkan Golshani   +7 more
doaj   +1 more source

Measurement of average decoding rates of the 61 sense codons in vivo

eLife, 2014
Most amino acids can be encoded by several synonymous codons, which are used at unequal frequencies. The significance of unequal codon usage remains unclear. One hypothesis is that frequent codons are translated relatively rapidly.
Justin Gardin, Rukhsana Yeasmin, Alisa Yurovsky, Ying Cai, Steve Skiena, Bruce Futcher   +5 more
doaj   +1 more source

The link between adjacent codon pairs and mRNA stability

BMC Genomics, 2017
Background Evidence in diverse organisms suggests that codon optimality is a major determinant of mRNA translation and degradation. Codon optimality is thought to act by modulating the efficiency of ribosome elongation.
Yuriko Harigaya, Roy Parker
doaj   +1 more source

On the Evolution of Codon Volatility [PDF]

Genetics, 2005
Abstract Volatility of a codon is defined as the probability that a random point mutation in the codon generates a nonsynonymous change. It has been proposed that higher-than-expected mean codon volatility of a gene indicates that positive selection for nonsynonymous changes has acted on the gene in the recent past.
openaire   +3 more sources

Context-dependent codon partition models provide significant increases in model fit in atpB and rbcL protein-coding genes

BMC Evolutionary Biology, 2011
Background Accurate modelling of substitution processes in protein-coding sequences is often hampered by the computational burdens associated with full codon models. Lately, codon partition models have been proposed as a viable alternative, mimicking the
Baele Guy, Van de Peer Yves, Vansteelandt Stijn   +2 more
doaj   +1 more source

In Arabidopsis thaliana codon volatility scores reflect GC3 composition rather than selective pressure

BMC Research Notes, 2012
Background Synonymous codon usage bias has typically been correlated with, and attributed to translational efficiency. However, there are other pressures on genomic sequence composition that can affect codon usage patterns such as mutational biases. This
O'Connell Mary J, Doyle Aisling M, Juenger Thomas E, Donoghue Mark TA, Keshavaiah Channa, Tuteja Reetu, Spillane Charles   +6 more
doaj   +1 more source