Context-dependent codon partition models provide significant increases in model fit in atpB and rbcL protein-coding genes
نویسندگان
چکیده
منابع مشابه
Regularities of context-dependent codon bias in eukaryotic genes.
Nucleotides surrounding a codon influence the choice of this particular codon from among the group of possible synonymous codons. The strongest influence on codon usage arises from the nucleotide immediately following the codon and is known as the N1 context. We studied the relative abundance of codons with N1 contexts in genes from four eukaryotes for which the entire genomes have been sequenc...
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Codon Usage in Hemoglobin Coding Genes
Shaanxi Province, China Hemoglobin is a protein responsible for the transport of oxygen. The preference of hemoglobin coding gene is analyzed by CodonW. The relationship between the A3 / (A3 + T3) and G3 / (G3 + C3) and the relationship between GC12 and GC3 are all investigated. Finally, the preference of hemoglobin coding gene is shown and discussed. The results show that codon use preference ...
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We develop novel methods for comparative genomics analysis of protein-coding genes using phylogenetic codon models, in pursuit of two main lines of biological investigation: First, we develop PhyloCSF, an algorithm based on empirical phylogenetic codon models to distinguish protein-coding and non-coding regions in multi-species genome alignments. We benchmark PhyloCSF to show that it outperform...
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ژورنال
عنوان ژورنال: BMC Evolutionary Biology
سال: 2011
ISSN: 1471-2148
DOI: 10.1186/1471-2148-11-145