{"title":"DeGeCI 1.1：线粒体基因组基因注释网络平台","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":72368,"journal":{"name":"Bioinformatics advances","volume":null,"pages":null},"PeriodicalIF":2.4000,"publicationDate":"2024-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"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\":72368,\"journal\":{\"name\":\"Bioinformatics advances\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":2.4000,\"publicationDate\":\"2024-05-13\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Bioinformatics advances\",\"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\":\"MATHEMATICAL & COMPUTATIONAL BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Bioinformatics advances","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":"MATHEMATICAL & COMPUTATIONAL BIOLOGY","Score":null,"Total":0}
DeGeCI 1.1: a web platform for gene annotation of mitochondrial genomes
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.
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