RCPdb: An evolutionary classification and codon usage database for repeat-containing proteins
نویسندگان
چکیده
منابع مشابه
Di-codon usage for classification of genes
Genes are often classified into biologically related groups so that inferences on their functions can be made. This paper demonstrates that the di-codon usage is a useful feature for gene classification and gives better classification accuracy than the codon usage. Our experiments with different classifiers show that support vector machines performs better than other classifiers in classifying ...
متن کاملSynonymous codon usage and selection on proteins
Selection pressures on proteins are usually measured by comparing homologous nucleotide sequences (Zuckerkandl and Pauling 1965). Recently we introduced a novel method, termed `volatility', to estimate selection pressures on protein sequences from their synonymous codon usage (Plotkin and Dushoff 2003, Plotkin et al 2004a). Here we provide a theoretical foundation for this approach. We derive t...
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WD40-repeat proteins, as one of the largest protein families, often serve as platforms to assemble functional complexes through the hotspot residues on their domain surfaces, and thus play vital roles in many biological processes. Consequently, it is highly required for researchers who study WD40 proteins and protein-protein interactions to obtain structural information of WD40 domains. Systema...
متن کاملCodon usage: Nature's roadmap to expression and folding of proteins
Biomedical and biotechnological research relies on processes leading to the successful expression and production of key biological products. High-quality proteins are required for many purposes, including protein structural and functional studies. Protein expression is the culmination of multistep processes involving regulation at the level of transcription, mRNA turnover, protein translation, ...
متن کاملClassification of Genes Based on Synonymous Codon Usage
Introduction The prediction of the function of a novel gene remains to be a challenging problem. Given a piece of coding sequence, one can deduce its function by finding homologous genes using sequence or protein structural alignment. One can also perform gene expression measurements or gene knockout experiments to determine the function of a gene. However, a gene may not have homology with any...
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ژورنال
عنوان ژورنال: Genome Research
سال: 2007
ISSN: 1088-9051
DOI: 10.1101/gr.6255407