ArticleScientific reports2017
Computational design of fully overlapping coding schemes for protein pairs and triplets.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Design of overlapping genes using deep generative models of protein sequences.bioRxiv : the preprint server for biology · 2025Article
- Base Pairing Promoted the Self-Organization of Genetic Coding, Catalysis, and Free-Energy Transduction.Life (Basel, Switzerland) · 2024Review
- Overlapping genes in natural and engineered genomes.Nature reviews. Genetics · 2022Review
- Biological factors in the synthetic construction of overlapping genes.BMC genomics · 2021Article
- Combining genetic algorithm with machine learning strategies for designing potent antimicrobial peptides.BMC bioinformatics · 2021Article
- Pentamers with Non-redundant Frames: Bias for Natural Circular Code Codons.Journal of molecular evolution · 2020Article
- Experimental solutions to problems defining the origin of codon-directed protein synthesis.Bio Systems · 2019Review
- Theoretical minimal RNA rings designed according to coding constraints mimic deamination gradients.Die Naturwissenschaften · 2019Article
- More Pieces of Ancient than Recent Theoretical Minimal Proto-tRNA-Like RNA Rings in Genes Coding for tRNA Synthetases.Journal of molecular evolution · 2019Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene pairs that overlap in their coding regions are rare except in viruses. They may occur transiently in gene creation and are of biotechnological interest. We have examined the possibility to encode an arbitrary pair of protein domains as a dual gene, with the shorter coding sequence completely embedded in the longer one. For 500 × 500 domain pairs (X, Y), we computationally designed homologous pairs (X', Y') coded this way, using an algorithm that provably maximizes the sequence similarity between (X', Y') and (X, Y). Three schemes were considered, with X' and Y' coded on the same or complementary strands. For 16% of the pairs, an overlapping coding exists where the level of homology of X', Y' to the natural proteins represents an E-value of 10
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