Table 1 Definitions and references for abbreviations and terms used in this paper
From: Meeting report: GenBank microbial genomic taxonomy workshop (12–13 May, 2015)
Term/abbreviation | Reference | Definition |
|---|---|---|
type | [11] | exemplar strain designated when a new name is described in the taxonomic literature |
proxytype | [1] | genome designated (by NCBI) to serve as a proxy for the type, for species that do not yet have a genome from type |
genome from type | [1] | genome sequence (complete or WGS) from a type strain |
sequence from type | [1] | GenBank sequence from a type strain (generally excluding components of genomes from type) |
ANI | pairwise average nucleotide identity between two genomes, measured across the alignable region. | |
AAI | [14] | average amino acid identity |
dDDH | [15] | digital DNA/DNA hybridization |
TETRA | [16] | tetranucleotide frequency distribution |
MLSA | [4] | multi-locus sequence analysis. ours is based on ribosomal protein sequences |
species complex | a group of closely related species which are difficult to distinguish by traditional methods | |
suppressed | a sequence entry that has been removed from Entrez, BLAST and the INSDC exchange. It is still retrievable by accession. http://www.insdc.org/documents/insdc-status-document | |
unverified | [17] | a sequence entry that has been flagged as problematic with the defline token UNVERIFIED. It is indexed in Entrez and exchanged by the INSDC, but is removed from BLAST. |
INSDC | International Nucleotide Sequence Database Collaboration, GenBank/ENA/DDBJ http://www.insdc.org/ |