{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/an-event-driven-approach-for-studying-gene","title":"An Event-Driven Approach for Studying Gene Block Evolution in Bacteria","arxiv_id":"1501.00302","date":"2015-02-24","proceeding":null,"authors":[],"abstract":"Motivation: Gene blocks are genes co-located on the chromosome. In many\ncases, genes blocks are conserved between bacterial species, sometimes as\noperons, when genes are co-transcribed. The conservation is rarely absolute:\ngene loss, gain, duplication, block splitting, and block fusion are frequently\nobserved. An open question in bacterial molecular evolution is that of the\nformation and breakup of gene blocks, for which several models have been\nproposed. These models, however, are not generally applicable to all types of\ngene blocks, and consequently cannot be used to broadly compare and study gene\nblock evolution. To address this problem we introduce an event-based method for\ntracking gene block evolution in bacteria. Results: We show here that the\nevolution of gene blocks in proteobacteria can be described by a small set of\nevents. Those include the insertion of genes into, or the splitting of genes\nout of a gene block, gene loss, and gene duplication. We show how the\nevent-based method of gene block evolution allows us to determine the\nevolutionary rate, and to trace the ancestral states of their formation. We\nconclude that the event-based method can be used to help us understand the\nformation of these important bacterial genomic structures. Availability: The\nsoftware is available under GPLv3 license on\nhttp://github.com/reamdc1/gene_block_evolution.git Supplementary online\nmaterial: http://iddo-friedberg.net/operon-evolution Contact: Iddo Friedberg\ni.friedberg@miamioh.edu","url_abs":"http://arxiv.org/abs/1501.00302v2","url_pdf":"http://arxiv.org/pdf/1501.00302v2.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"an-event-driven-approach-for-studying-gene","repo_url":"https://github.com/reamdc1/gene_block_evolution","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[{"task_slug":"open-question","task_name":"Open-Ended Question Answering"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}