a database designed for the purpose of accelerating and simplifying the description of Earth's microbial diversity at a precision that includes, but also goes beyond, named species. Users can circumscribe, describe, and name any group of bacteria (which we call LINgroups) at or below the genus level, even if the group consists of a single clonal lineage. This is simply done by selecting genomes of strains belonging to the taxon, adding a description, and providing a name. Validly published species names need to be linked to a peer-reviewed publication. Users can also upload genomes to place them precisely into the genome similarity framework together with all genomes already in GenomeRxiv to aid in precise strain identification and classification. GenomeRxiv can also be searched using short gene sequences to easily identify unknown strains even if their whole genome sequence is not available.
Note that genomeRxiv is still under development. We appreciate your patience and your help in improving genomeRxiv by uploading genome sequences and defining LINgroups. Please, e-mail linbase@vt.edu with any technical questions or vinatzer@vt.edu with any general questions or suggestions.
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If you have found genomeRxiv or LINbase useful, please cite:
LINbase: a web server for genome-based identification of prokaryotes as members
of crowdsourced taxa
Tian Long, Chengjie Huang, Reza Mazloom, Lenwood S. Heath, and Boris A. Vinatzer
Nucleic Acids Research (2020)
doi:10.1093/nar/gkaa190.
A proposal for a portal to make earth’s microbial diversity easily accessible and
searchable
Boris A Vinatzer, Long Tian, Lenwood S Heath
Antonie van Leeuwenhoek (2017) doi:
10.1007/s10482-017-0849-z.
A proposal for a genome similarity-based taxonomy for plant-pathogenic bacteria that is
sufficiently precise to reflect phylogeny, host range, and outbreak affiliation applied to
Pseudomonas syringae sensu lato as a proof of concept
Boris A Vinatzer, Alexandra J Weisberg, Caroline L Monteil, Haitham A Elmarakeby, Samuel K Sheppard,
Lenwood S Heath
Phytopathology (2016) doi:
10.1094/PHYTO-07-16-0252-R.
Similarity-based codes sequentially assigned to ebolavirus genomes are informative of species
membership, associated outbreaks, and transmission chains
Alexandra J Weisberg, Haitham A Elmarakeby, Lenwood S Heath, Boris A Vinatzer
Open forum infectious diseases (2015) doi:
10.1093/ofid/ofv024.
A system to automatically classify and name any individual genome-sequenced organism
independently of current biological classification and nomenclature
Haitham Marakeby, Eman Badr, Hanaa Torkey, Yuhyun Song, Caroline L Monteil, Lenwood S Heath, Boris A
Vinatzer
PLoS One (2014) doi:
10.1371/journal.pone.0089142.