{"doi":"10.3233/isb-00286","title":"Frameshift Signals in Genes Associated with the Circular \t\t\t Code","abstract":"<jats:p>Three sets of 20 trinucleotides are preferentially associated with the reading frames and their 2 shifted frames of both eukaryotic and prokaryotic genes. These 3 sets are circular codes. They allow retrieval of any frame in genes (containing these circular code words), locally anywhere in the 3 frames and in particular without start codons in the reading frame, and automatically with the reading of a few nucleotides. The circular code in the reading frame, noted X, which can deduce the 2 other circular codes in the shifted frames by permutation, is the information used for analysing frameshift genes, i.e. genes with a change of reading frame during translation. This work studies the circular code signal around their frameshift sites. Two scoring methods are developed, a function P based on this code X and a function Q based both on this code X and the 4 trinucleotides with identical nucleotides. They detect a significant correlation between the code X and the −1 frameshift signals in both eukaryotic and prokaryotic genes, and the +1 frameshift signals in eukaryotic genes.</jats:p>","journal":"In Silico Biology: Journal of Biological Systems Modeling and Multi-Scale Simulation","year":2007,"id":598308,"datarank":0.5244761342199721,"base_score":3.4965075614664802,"endowment":3.4965075614664802,"self_citation_contribution":0.5244761342199721,"citation_network_contribution":0.0,"self_endowment_contribution":0.5244761342199721,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":32,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1533020,"name":"Gabriel Frey","orcid":null,"position":1,"is_corresponding":false},{"id":1533022,"name":"Christian J. 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The circular code in the reading frame, noted X, which can deduce the 2 other circular codes in the shifted frames by permutation, is the information used for analysing frameshift genes, i.e. genes with a change of reading frame during translation. This work studies the circular code signal around their frameshift sites. Two scoring methods are developed, a function P based on this code X and a function Q based both on this code X and the 4 trinucleotides with identical nucleotides. They detect a significant correlation between the code X and the −1 frameshift signals in both eukaryotic and prokaryotic genes, and the +1 frameshift signals in eukaryotic genes.</jats:p>","is_dataset_classified":null,"base_score":3.4965075614664802,"endowment":3.4965075614664802,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"17688441","pmcid":null,"openalex_id":"https://openalex.org/W2104816745","authors":[],"funders":[],"total_grants":0,"fwci":0.2514,"citation_percentile":0.57128946,"influential_citations":0,"citation_trend":[{"year":2012,"count":4},{"year":2013,"count":4},{"year":2014,"count":1},{"year":2015,"count":3},{"year":2016,"count":2},{"year":2017,"count":4},{"year":2018,"count":3},{"year":2019,"count":4},{"year":2020,"count":5}],"oa_status":"closed","license":"https://journals.sagepub.com/page/policies/text-and-data-mining-license","oa_locations":[{"url":"https://journals.sagepub.com/doi/pdf/10.3233/ISB-00286","host_type":"publisher"},{"url":"https://doi.org/10.3233/isb-00286","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/17688441","host_type":"repository"}],"fields_of_study":["RNA and protein synthesis mechanisms","Machine Learning in Bioinformatics","Genomics and Phylogenetic Studies"],"mesh_terms":["Animals","Codon","DNA","Eukaryotic Cells","Genes","Genetic Code","Humans","Models, Genetic","Prokaryotic Cells","Frameshifting, Ribosomal"],"keywords":["Frameshift mutation","Code (set theory)","Genetics","Gene","Biology","Computational biology","Mathematics","Computer science","Mutation","Programming language"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Quality Education"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-28T15:28:00.427537Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}