{"title":"DeGeCI 1.1: a web platform for gene annotation of mitochondrial genomes","authors":"Lisa Fiedler, Matthias Bernt, Martin Middendorf","doi":"10.1093/bioadv/vbae072","DOIUrl":null,"url":null,"abstract":"\n \n \n DeGeCI is a command line tool that generates fully automated de novo gene predictions from mitochondrial nucleotide sequences by using a reference database of annotated mitogenomes which is represented as a de Bruijngraph. The input genome is mapped to this graph, creating a subgraph, which is then post-processed by a clustering routine. Version 1.1 of DeGeCI offers a web front-end for GUI-based input. It also introduces a new taxonomic filter pipeline that allows the species in the reference database to be restricted to a user-specified taxonomic classification and allows for gene boundary optimization when providing the translation table of the input genome.\n \n \n \n The web platform is accessible at https://degeci.informatik.uni-leipzig.de. Source code is freely available at https://git.informatik.uni-leipzig.de/lfiedler/degeci.\n","PeriodicalId":2,"journal":{"name":"ACS Applied Bio Materials","volume":"120 12","pages":""},"PeriodicalIF":4.7000,"publicationDate":"2024-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"ACS Applied Bio Materials","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1093/bioadv/vbae072","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"MATERIALS SCIENCE, BIOMATERIALS","Score":null,"Total":0}
引用次数: 0
Abstract
DeGeCI is a command line tool that generates fully automated de novo gene predictions from mitochondrial nucleotide sequences by using a reference database of annotated mitogenomes which is represented as a de Bruijngraph. The input genome is mapped to this graph, creating a subgraph, which is then post-processed by a clustering routine. Version 1.1 of DeGeCI offers a web front-end for GUI-based input. It also introduces a new taxonomic filter pipeline that allows the species in the reference database to be restricted to a user-specified taxonomic classification and allows for gene boundary optimization when providing the translation table of the input genome.
The web platform is accessible at https://degeci.informatik.uni-leipzig.de. Source code is freely available at https://git.informatik.uni-leipzig.de/lfiedler/degeci.
期刊介绍：
ACS Applied Bio Materials is an interdisciplinary journal publishing original research covering all aspects of biomaterials and biointerfaces including and beyond the traditional biosensing, biomedical and therapeutic applications.
The journal is devoted to reports of new and original experimental and theoretical research of an applied nature that integrates knowledge in the areas of materials, engineering, physics, bioscience, and chemistry into important bio applications. The journal is specifically interested in work that addresses the relationship between structure and function and assesses the stability and degradation of materials under relevant environmental and biological conditions.
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