Comparative context analysis of codon pairs on an ORFeome scale
Open accessAbstract
Codon context is an important feature of gene primary structure that modulates mRNA decoding accuracy. We have developed an analytical software package and a graphical interface for comparative codon context analysis of all the open reading frames in a genome (the ORFeome). Using the complete ORFeome sequences of Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans and Escherichia coli, we show that this methodology permits large-scale codon context comparisons and provides new insight on the rules that govern the evolution of codon-pair context.
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Codon pair preference has been found in every species studied and can be radically dissimilar between phylogenetically distant species.
“Codon pair preference has been found in every species studied and can be radically dissimilar between phylogenetically distant species (Moura et al., 2005;Mueller et al., 2010).”
From Codon Pair Bias Is a Direct Consequence of Dinucleotide Bias (2016) · cites this paper as Moura et al., 2005
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Self-citationWang, L., Zhao, H., Wang, Z., Ding, S., Qin, L., Jiang, R., Deng, X., He, Z. J., & Li, L. (2023) · Genes · doi:10.3390/genes14091712 · Cited by 7 · see citing works
Pal, A., Banerjee, R., Mondal, U., Mukhopadhyay, S., & Bothra, A. (2015) · PLoS ONE · doi:10.1371/journal.pone.0118245 · Cited by 7 · see citing works
Behura, S. K., & Severson, D. W. (2014) · Molecular Genetics and Genomics · doi:10.1007/s00438-014-0857-x · Cited by 6 · see citing works
Analysis of synonymous codon usage bias in Ancylostoma ceylanicum
Singh, R. (2021) · Gene Reports · doi:10.1016/j.genrep.2021.101290 · Cited by 6 · see citing works
Freitas, A. V., Afreixo, V. M. A., Pinheiro, M. M., Oliveira, J. L., Moura, G., & Santos, M. A. S. (2011) · Statistical Analysis and Data Mining The ASA Data Science Journal · doi:10.1002/sam.10104 · Cited by 6 · see citing works
Self-citationCodingMotif: exact determination of overrepresented nucleotide motifs in coding sequences
Ding, Y., Lorenz, W. A., & Chuang, J. H. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-32 · Cited by 6 · see citing works
Computational tools for synthetic gene optimization
Cheema, N., Papamichail, G. P., & Papamichail, D. (2022) · Elsevier eBooks · doi:10.1016/b978-0-12-824469-2.00018-x · Cited by 5 · see citing works
HPVomics: An integrated resource for the human papillomavirus epitome and therapeutics
Gupta, A., & Kumar, M. (2020) · Genomics · doi:10.1016/j.ygeno.2020.08.025 · Cited by 4 · see citing works
Khandia, R., Pandey, M. K., Khan, A. A., Baklanov, I. S., Alanazi, A. M., Nepali, P., Gurjar, P., & Choudhary, O. P. (2024) · Annals of Medicine and Surgery · doi:10.1097/ms9.0000000000001465 · Cited by 4 · see citing works
An Insight into Codon Pattern Analysis of Autophagy Genes Associated with Virus Infection
Singhal, S., Kumar, U., Alqahtani, T., Rzhepakovsky, I. V., Khandia, R., Pandey, M. K., Alqahtani, S., Alharbi, H. M., & Kamal, M. A. (2023) · Current Pharmaceutical Design · doi:10.2174/1381612829666230418093308 · Cited by 3 · see citing works
Jiao, L., Jing, Z., Zhang, W., Su, X., Yan, H., & Tian, S. (2024) · Journal of Alzheimer s Disease · doi:10.3233/jad-231142 · Cited by 3 · see citing works
Visualizing Codon Usage Within and Across Genomes: Concepts and Tools
Ostash, B. O., & Anisimova, M. O. (2020) · Algorithms for intelligent systems · doi:10.1007/978-981-15-2445-5_13 · Cited by 3 · see citing works
Radomski, J. P., & Słonimski, P. P. (2009) · Comptes Rendus Biologies · doi:10.1016/j.crvi.2008.11.008 · Cited by 3 · see citing works
Coding Biases and Viral Fitness
Bosch, A., Mueller, S., & Pintó, R. M. (2014) · ASM Press eBooks · doi:10.1128/9781555816698.ch17 · Cited by 3 · see citing works
Mixture models of geometric distributions in genomic analysis of inter-nucleotide distances
Freitas, A. V., Afreixo, V. M. A., & Cruz, S. E. (2013) · Statistics Optimization & Information Computing · doi:10.19139/6 · Cited by 3 · see citing works
Self-citationComputational and Statistical Methodologies for ORFeome Primary Structure Analysis
Moura, G., Pinheiro, M. M., Freitas, A. V., Oliveira, J. L., & Santos, M. A. S. (2007) · Methods in molecular biology · doi:10.1007/978-1-59745-514-5_28 · Cited by 3 · see citing works
Self-citationCodon usage bias analysis of genes linked with esophagus cancer
Bordoloi, H. (2021) · Bioinformation · doi:10.6026/97320630017731 · Cited by 2 · see citing works
Khandia, R., Gurjar, P., Romashchenko, V. A., Al‐Hussain, S. A., Alexiou, A. T., Zouganelis, G. D., & Zaki, M. E. A. (2024) · Journal of Alzheimer s Disease · doi:10.3233/jad-240158 · Cited by 2 · see citing works
Analysing the Evolution of Repetitive Strands in Genomes
Lousado, J. P., Oliveira, J. L., Moura, G. R., & Santos, M. A. S. (2009) · Lecture notes in computer science · doi:10.1007/978-3-642-02481-8_159 · Cited by 2 · see citing works
Self-citationMixture models of geometric distributions in genomic analysis of inter-nucleotide distances
Freitas, A. V., Afreixo, V. M. A., & Escudeiro, S. (2013) · Statistics Optimization & Information Computing · doi:10.19139/soic.v1i1.6 · Cited by 2 · see citing works
Self-citationChandan, J., Gupta, S., Nisa, S., Babu, V., & Singh, R. (2023) · Gene Reports · doi:10.1016/j.genrep.2023.101805 · Cited by 2 · see citing works
Nisa, S., Gupta, S., & Singh, R. (2023) · Physiological and Molecular Plant Pathology · doi:10.1016/j.pmpp.2023.102131 · Cited by 2 · see citing works
Prabha, R., Singh, D. P., & Rai, A. K. (2015) · International Journal of Bioinformatics Research and Applications · doi:10.1504/ijbra.2015.068088 · Cited by 1 · see citing works
On the molecular mechanism of the evolution of genetic code alterations
Gomes, A. C., Lima-Costa, T., Carreto, L. C., & Santos, M. A. S. (2006) · Molecular Biology · doi:10.1134/s002689330604008x · Cited by 1 · see citing works
Self-citationTavares, J. F., Davis, N., Poim, A., Reis, A., Kellner, S. M., Sousa, I., Soares, A. R., Moura, G., Dedon, P. C., & Santos, M. A. S. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.13.200121 · Cited by 1 · see citing works
Self-citationCramér Coefficient in Genome Evolution
Afreixo, V. M. A., & Freitas, A. V. (2010) · Advances in intelligent and soft computing · doi:10.1007/978-3-642-13214-8_13
Self-citationStudying the Evolution of Codon Context in Conserved Gene Sequences
Pinheiro, M. M., Oliveira, J. L., Moura, G., & Santos, M. A. S. (2008) · Biocomputation, Bioinformatics, and Biomedical Technologies · doi:10.1109/biotechno.2008.18
Self-citationAnálise de repetições em dados biológicos
Lousado, J. P., & Oliveira, J. L. (2010) · Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)
Self-citationPal, A., Bothra, A., & Mukhopadhyay, S. (2016) · International Conference on Bioinformatics and Systems Biology (BSB) · doi:10.1109/bsb.2016.7552130
Modulation of Translation Efficiency in S. cerevisiae by Codon Pairs and mRNA Structure
Gamble, C. E. (2016) · ResearchWorks at the University of Washington (University of Washington)
Genomic insights into codon usage bias in Cannabis sativa and pathogenic interactions
Nisa, S., Ghora, B., Sharma, V., Chandan, J., Singh, P. P., Hassan, M. R., & Singh, R. (2024) · Ecological Genetics and Genomics · doi:10.1016/j.egg.2024.100296
Ribeiro, D. R., Nunes, A., Monti, M., Llovera, L., Berg, M., Kerkhoff, K., Pereira, M., Guimarães, A. R., Kaiser, S., Novoa, E. M., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.04.21.719891
Expression of mannanases in fermentative yeasts.
Fouche, N. (2009) · SUNScholar (Stellenbosch University)
Intermittency and Irreversibility in the Soil-Plant-Atmosphere System
Rigby, J. R. (2009) · DukeSpace (Duke University)
- Authors
- Moura, G., Pinheiro, M., Silva, R., Miranda, I., Afreixo, V., Dias, G., Freitas, A., Oliveira, J. L., & Santos, M. A.
- Affiliations
- University of Aveiro (PT)
- Corresponding author
- Santos, Manuel AS
- ORCID
- Venue
- Genome Biology
- Published
- 2005-02-15
- Volume
- 6
- Issue
- 3
- Pages
- R28-R28
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC1088947
- OpenAlex
- W2128742161
- Cited by
- 90
- References
- 55
- Citations by year
- 2026: 1 · 2024: 4 · 2023: 6 · 2022: 4 · 2021: 7 · 2020: 7 · 2018: 1 · 2017: 4 · 2016: 10 · 2015: 6 · 2014: 7 · 2013: 5 · 2012: 4
- FWCI
- 1.39
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed (publishedVersion)
- Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT) (submittedVersion, other-oa)
- Funders
- Fundação para a Ciência e a Tecnologia (POCTI/BME/39030/2001, SFRH/BPD/7195/2001)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Keywords
- codon context, open reading frames, ORFeome, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans, Escherichia coli, comparative genomics
- MeSH terms
- Candida albicans, Codon, Escherichia coli, RNA, Messenger, Saccharomyces cerevisiae, Schizosaccharomyces, Software, Cluster Analysis, Open Reading Frames, Evolution, Molecular, Computational Biology, Genomics
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