ToxCodAn-Genome: an automated pipeline for toxin-gene annotation in genome assembly of venomous lineages

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dc.contributor(LETA) Lab. Toxinologia Aplicadapt_BR
dc.contributor(CeTICS) Centro de Toxinas, Resposta-imune e Sinalização Celularpt_BR
dc.contributor.authorNachtigall, Pedro Gabrielpt_BR
dc.contributor.authorDurham, Alan M.pt_BR
dc.contributor.authorRokyta, Darin R.pt_BR
dc.contributor.authorJunqueira-de-Azevedo, Inácio de Loiola Meirellespt_BR
dc.date.accessioned2024-02-21T13:37:15Z-
dc.date.available2024-02-21T13:37:15Z-
dc.date.issued2024pt_BR
dc.identifier.urihttps://repositorio.butantan.gov.br/handle/butantan/5255-
dc.description.abstractBackground: The rapid development of sequencing technologies resulted in a wide expansion of genomics studies using venomous lineages. This facilitated research focusing on understanding the evolution of adaptive traits and the search for novel compounds that can be applied in agriculture and medicine. However, the toxin annotation of genomes is a laborious and time-consuming task, and no consensus pipeline is currently available. No computational tool currently exists to address the challenges specific to toxin annotation and to ensure the reproducibility of the process. Results: Here, we present ToxCodAn-Genome, the first software designed to perform automated toxin annotation in genomes of venomous lineages. This pipeline was designed to retrieve the full-length coding sequences of toxins and to allow the detection of novel truncated paralogs and pseudogenes. We tested ToxCodAn-Genome using 12 genomes of venomous lineages and achieved high performance on recovering their current toxin annotations. This tool can be easily customized to allow improvements in the final toxin annotation set and can be expanded to virtually any venomous lineage. ToxCodAn-Genome is fast, allowing it to run on any personal computer, but it can also be executed in multicore mode, taking advantage of large high-performance servers. In addition, we provide a guide to direct future research in the venomics field to ensure a confident toxin annotation in the genome being studied. As a case study, we sequenced and annotated the toxin repertoire of Bothrops alternatus, which may facilitate future evolutionary and biomedical studies using vipers as models. Conclusions: ToxCodAn-Genome is suitable to perform toxin annotation in the genome of venomous species and may help to improve the reproducibility of further studies. ToxCodAn-Genome and the guide are freely available at https://github.com/pedronachtigall/T oxCodAn-Genome.pt_BR
dc.format.extent1-17pt_BR
dc.language.isoEnglishpt_BR
dc.relation.ispartofGigaSciencept_BR
dc.rightsOpen accesspt_BR
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/pt_BR
dc.titleToxCodAn-Genome: an automated pipeline for toxin-gene annotation in genome assembly of venomous lineagespt_BR
dc.typeArticlept_BR
dc.rights.licenseCC BYpt_BR
dc.identifier.doi10.1093/gigascience/giad116pt_BR
dc.identifier.urlhttps://doi.org/10.1093/gigascience/giad116pt_BR
dc.contributor.externalFlorida State Universitypt_BR
dc.contributor.external(USP) Universidade de São Paulopt_BR
dc.identifier.citationvolume13pt_BR
dc.subject.keywordWGSpt_BR
dc.subject.keywordDNA-seqpt_BR
dc.subject.keywordgenome annotationpt_BR
dc.subject.keywordgene modelpt_BR
dc.subject.keywordvenomicspt_BR
dc.relation.ispartofabbreviatedGigaSciencept_BR
dc.identifier.citationabntv. 13, 1-17, 2024.pt_BR
dc.identifier.citationvancouver2024; 13:1-17pt_BR
dc.contributor.butantanJunqueira-de-Azevedo, Inácio de Loiola Meirelles|:Pesquisador|:(LETA) Lab. Toxinologia Aplicadapt_BR
dc.identifier.bvsccBR78.1pt_BR
dc.identifier.bvsdbIBProdpt_BR
dc.description.dbindexedYespt_BR
item.fulltextCom Texto completo-
item.languageiso639-1English-
item.grantfulltextopen-
item.openairetypeArticle-
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