Paper| Year: | 2018 |
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| Author(s): | LM. Rodriguez-R, S. Gunturu, WT. Harvey, R. Rossello-Mora, JM. Tiejde, JR. Cole, KT. Konstantinidis |
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| Title: | The microbial genomes atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level |
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| Journal: | NUCLEIC ACIDS RESEARCH |
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| ISSN: | 0305-1048 |
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| JCR Impact Factor: | 11.147 |
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| Volume: | 46 |
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| Pages: | 282-288 |
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| D.O.I.: | 10.1093/nar/gky467 |
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| Web: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6031002/ |
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| Abstract: | The small subunit ribosomal RNA gene (16S rRNA) has been successfully
used to catalogue and study the diversity of prokaryotic species and
communities but it offers limited resolution at the species and finer
levels, and cannot represent the whole-genome diversity and fluidity. To
overcome these limitations, we introduced the Microbial Genomes Atlas
(MiGA), a webserver that allows the classification of an unknown query
genomic sequence, complete or partial, against all taxonomically
classified taxa with available genome sequences, as well as comparisons
to other related genomes including uncultivated ones, based on the
genome-aggregate Average Nucleotide and Amino Acid Identity (ANI/AAI)
concepts. MiGA integrates best practices in sequence quality trimming
and assembly and allows input to be raw reads or assemblies from isolate
genomes, single-cell sequences, and metagenome-assembled genomes
(MAGs). Further, MiGA can take as input hundreds of closely related
genomes of the same or closely related species (a so-called ‘Clade
Project’) to assess their gene content diversity and evolutionary
relationships, and calculate important clade properties such as the
pangenome and core gene sets. Therefore, MiGA is expected to facilitate a
range of genome-based taxonomic and diversity studies, and quality
assessment across environmental and clinical settings |
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Related staffRamon Rosselló MóraRelated departmentsAnimal and Microbial BiodiversityRelated projectsSALPLOMA CTA 146Related research groupsEnvironmental Microbiology
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