Sketched reference databases for genome-based taxonomy and comparative genomics
Autor(a) principal: | |
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Data de Publicação: | 2024 |
Outros Autores: | |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Brazilian Journal of Biology |
Texto Completo: | http://old.scielo.br/scielo.php?script=sci_arttext&pid=S1519-69842024000100405 |
Resumo: | Abstract The analysis of curated genomic, metagenomic and proteomic data is of paramount importance in the fields of biology, medicine, education, and bioinformatics. Although this type of data is usually hosted in raw format on free international repositories, the full access requires lots of computing power and large storage disk space for the domestic user. The purpose of the study is to offer a comprehensive set of microbial genomic and proteomic reference databases in an accessible and easy-to-use form to the scientific community and demonstrate its advantages and usefulness. Also, we present a case study on the applicability of the sketched data, for the determination of overall genomic coherence between two members of the Brucellacea family, which suggests they belong to the same genomospecies that remain as discrete ecotypes. A representative set of genomes, proteomes (from type material), and metagenomes were directly collected from the NCBI Assembly database and Genome Taxonomy Database (GTDB), associated with the major groups of Bacteria, Archaea, Virus, and Fungi. Sketched databases were subsequently created and stored on handy reduced representations by using the MinHash algorithm implemented in Mash software. The obtained dataset contains more than 133 GB of space disk reduced to 883.25 MB and represents 125,110 genomics/proteomic records from eight informative contexts, which have been prefiltered to make them accessible, usable, and user-friendly with limited computational resources. Potential uses of these sketched databases are discussed, including but not limited to microbial species delimitation, estimation of genomic distances and genomic novelties, paired comparisons between proteomes, genomes, and metagenomes; phylogenetic neighbor’s exploration and selection, among others. |
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Sketched reference databases for genome-based taxonomy and comparative genomicsmicrobial Mash databasegenomic distancegenome containmenttype materialmicrobial taxonomyAbstract The analysis of curated genomic, metagenomic and proteomic data is of paramount importance in the fields of biology, medicine, education, and bioinformatics. Although this type of data is usually hosted in raw format on free international repositories, the full access requires lots of computing power and large storage disk space for the domestic user. The purpose of the study is to offer a comprehensive set of microbial genomic and proteomic reference databases in an accessible and easy-to-use form to the scientific community and demonstrate its advantages and usefulness. Also, we present a case study on the applicability of the sketched data, for the determination of overall genomic coherence between two members of the Brucellacea family, which suggests they belong to the same genomospecies that remain as discrete ecotypes. A representative set of genomes, proteomes (from type material), and metagenomes were directly collected from the NCBI Assembly database and Genome Taxonomy Database (GTDB), associated with the major groups of Bacteria, Archaea, Virus, and Fungi. Sketched databases were subsequently created and stored on handy reduced representations by using the MinHash algorithm implemented in Mash software. The obtained dataset contains more than 133 GB of space disk reduced to 883.25 MB and represents 125,110 genomics/proteomic records from eight informative contexts, which have been prefiltered to make them accessible, usable, and user-friendly with limited computational resources. Potential uses of these sketched databases are discussed, including but not limited to microbial species delimitation, estimation of genomic distances and genomic novelties, paired comparisons between proteomes, genomes, and metagenomes; phylogenetic neighbor’s exploration and selection, among others.Instituto Internacional de Ecologia2024-01-01info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersiontext/htmlhttp://old.scielo.br/scielo.php?script=sci_arttext&pid=S1519-69842024000100405Brazilian Journal of Biology v.84 2024reponame:Brazilian Journal of Biologyinstname:Instituto Internacional de Ecologia (IIE)instacron:IIE10.1590/1519-6984.256673info:eu-repo/semantics/openAccessSánchez-Reyes,A.Fernández-López,M. G.eng2022-11-08T00:00:00Zoai:scielo:S1519-69842024000100405Revistahttps://www.scielo.br/j/bjb/https://old.scielo.br/oai/scielo-oai.phpbjb@bjb.com.br||bjb@bjb.com.br1678-43751519-6984opendoar:2022-11-08T00:00Brazilian Journal of Biology - Instituto Internacional de Ecologia (IIE)false |
dc.title.none.fl_str_mv |
Sketched reference databases for genome-based taxonomy and comparative genomics |
title |
Sketched reference databases for genome-based taxonomy and comparative genomics |
spellingShingle |
Sketched reference databases for genome-based taxonomy and comparative genomics Sánchez-Reyes,A. microbial Mash database genomic distance genome containment type material microbial taxonomy |
title_short |
Sketched reference databases for genome-based taxonomy and comparative genomics |
title_full |
Sketched reference databases for genome-based taxonomy and comparative genomics |
title_fullStr |
Sketched reference databases for genome-based taxonomy and comparative genomics |
title_full_unstemmed |
Sketched reference databases for genome-based taxonomy and comparative genomics |
title_sort |
Sketched reference databases for genome-based taxonomy and comparative genomics |
author |
Sánchez-Reyes,A. |
author_facet |
Sánchez-Reyes,A. Fernández-López,M. G. |
author_role |
author |
author2 |
Fernández-López,M. G. |
author2_role |
author |
dc.contributor.author.fl_str_mv |
Sánchez-Reyes,A. Fernández-López,M. G. |
dc.subject.por.fl_str_mv |
microbial Mash database genomic distance genome containment type material microbial taxonomy |
topic |
microbial Mash database genomic distance genome containment type material microbial taxonomy |
description |
Abstract The analysis of curated genomic, metagenomic and proteomic data is of paramount importance in the fields of biology, medicine, education, and bioinformatics. Although this type of data is usually hosted in raw format on free international repositories, the full access requires lots of computing power and large storage disk space for the domestic user. The purpose of the study is to offer a comprehensive set of microbial genomic and proteomic reference databases in an accessible and easy-to-use form to the scientific community and demonstrate its advantages and usefulness. Also, we present a case study on the applicability of the sketched data, for the determination of overall genomic coherence between two members of the Brucellacea family, which suggests they belong to the same genomospecies that remain as discrete ecotypes. A representative set of genomes, proteomes (from type material), and metagenomes were directly collected from the NCBI Assembly database and Genome Taxonomy Database (GTDB), associated with the major groups of Bacteria, Archaea, Virus, and Fungi. Sketched databases were subsequently created and stored on handy reduced representations by using the MinHash algorithm implemented in Mash software. The obtained dataset contains more than 133 GB of space disk reduced to 883.25 MB and represents 125,110 genomics/proteomic records from eight informative contexts, which have been prefiltered to make them accessible, usable, and user-friendly with limited computational resources. Potential uses of these sketched databases are discussed, including but not limited to microbial species delimitation, estimation of genomic distances and genomic novelties, paired comparisons between proteomes, genomes, and metagenomes; phylogenetic neighbor’s exploration and selection, among others. |
publishDate |
2024 |
dc.date.none.fl_str_mv |
2024-01-01 |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://old.scielo.br/scielo.php?script=sci_arttext&pid=S1519-69842024000100405 |
url |
http://old.scielo.br/scielo.php?script=sci_arttext&pid=S1519-69842024000100405 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
10.1590/1519-6984.256673 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
text/html |
dc.publisher.none.fl_str_mv |
Instituto Internacional de Ecologia |
publisher.none.fl_str_mv |
Instituto Internacional de Ecologia |
dc.source.none.fl_str_mv |
Brazilian Journal of Biology v.84 2024 reponame:Brazilian Journal of Biology instname:Instituto Internacional de Ecologia (IIE) instacron:IIE |
instname_str |
Instituto Internacional de Ecologia (IIE) |
instacron_str |
IIE |
institution |
IIE |
reponame_str |
Brazilian Journal of Biology |
collection |
Brazilian Journal of Biology |
repository.name.fl_str_mv |
Brazilian Journal of Biology - Instituto Internacional de Ecologia (IIE) |
repository.mail.fl_str_mv |
bjb@bjb.com.br||bjb@bjb.com.br |
_version_ |
1752129891843702784 |