ArticleBioinformatics (Oxford, England)2012
Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Uncovering position-specific patterns in codon and codon-pair usage in candidate genes associated with blood coagulation diseases.NAR genomics and bioinformatics · 2025Article
- Codon-specific ribosome stalling reshapes translational dynamics during branched-chain amino acid starvation.Genome biology · 2025Article
- Codon usage bias in yeasts and its correlation with gene expression, growth temperature, and protein structure.Frontiers in microbiology · 2024Article
- Mechanisms governing codon usage bias and the implications for protein expression in the chloroplast of Chlamydomonas reinhardtii.The Plant journal : for cell and molecular biology · 2022Review
- Identification of conserved slow codons that are important for protein expression and function.RNA biology · 2021Article
- A Code Within a Code: How Codons Fine-Tune Protein Folding in the Cell.Biochemistry. Biokhimiia · 2021Review
- The effects of codon bias and optimality on mRNA and protein regulation.Cellular and molecular life sciences : CMLS · 2021Review
- Translational Control by Ribosome Pausing in Bacteria: How a Non-uniform Pace of Translation Affects Protein Production and Folding.Frontiers in microbiology · 2020Review
- A pair of non-optimal codons are necessary for the correct biosynthesis of theRoyal Society open science · 2019Article
- Molecular Modelling and Evaluation of Hidden Information in ABCB11 Gene Mutations.Journal of biomedical physics & engineering · 2019Article
- In-silico Evaluation of Rare Codons and their Positions in the Structure of ATP8b1 Gene.Journal of biomedical physics & engineering · 2019Article
- Dynamics of translation can determine the spatial organization of membrane-bound proteins and their mRNA.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Evidence of evolutionary selection for cotranslational folding.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Integrated analysis of individual codon contribution to protein biosynthesis reveals a new approach to improving the basis of rational gene design.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- Widespread position-specific conservation of synonymous rare codons within coding sequences.PLoS computational biology · 2017Article
- Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes.Computational and structural biotechnology journal · 2017Article
- The Yin and Yang of codon usage.Human molecular genetics · 2016Review
- Bioinformatic Identification of Rare Codon Clusters (RCCs) in HBV Genome and Evaluation of RCCs in Proteins Structure of Hepatitis B Virus.Hepatitis monthly · 2016Article
- Bioinformatic Analysis of Codon Usage and Phylogenetic Relationships in Different Genotypes of the Hepatitis C Virus.Hepatitis monthly · 2016Article
- Techniques for the Analysis of Protein-Protein Interactions in Vivo.Plant physiology · 2016Review
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3 authors.
Funding
Abstract
motivationAn increasing amount of evidence from experimental and computational analysis suggests that rare codon clusters are functionally important for protein activity. Most of the studies on rare codon clusters were performed on a limited number of proteins or protein families. In the present study, we present the Sherlocc program and how it can be used for large scale protein family analysis of evolutionarily conserved rare codon clusters and their relation to protein function and structure. This large-scale analysis was performed using the whole Pfam database covering over 70% of the known protein sequence universe. Our program Sherlocc, detects statistically relevant conserved rare codon clusters and produces a user-friendly HTML output.
resultsStatistically significant rare codon clusters were detected in a multitude of Pfam protein families. The most statistically significant rare codon clusters were predominantly identified in N-terminal Pfam families. Many of the longest rare codon clusters are found in membrane-related proteins which are required to interact with other proteins as part of their function, for example in targeting or insertion. We identified some cases where rare codon clusters can play a regulating role in the folding of catalytically important domains. Our results support the existence of a widespread functional role for rare codon clusters across species. Finally, we developed an online filter-based search interface that provides access to Sherlocc results for all Pfam families. AVAILABILITY: The Sherlocc program and search interface are open access and are available at http://bcb.med.usherbrooke.ca
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