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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 5

AppIndels.com server: a web-based tool for the identification of known taxon-specific conserved signature indels in genome sequences. Validation of its usefulness by predicting the taxonomic affiliation of >700 unclassified strains of species Open Access

A corrigendum to this paper has been published here.

Abstract

Taxon-specific conserved signature indels (CSIs) in genes/proteins provide reliable molecular markers (synapomorphies) for unambiguous demarcation of taxa of different ranks in molecular terms and for genetic, biochemical and diagnostic studies. Because of their predictive abilities, the shared presence of known taxon-specific CSIs in genome sequences has proven useful for taxonomic purposes. However, the lack of a convenient method for identifying the presence of known CSIs in genome sequences has limited their utility for taxonomic and other studies. We describe here a web-based tool/server (AppIndels.com) that identifies the presence of known and validated CSIs in genome sequences and uses this information for predicting taxonomic affiliation. The utility of this server was tested by using a database of 585 validated CSIs, which included 350 CSIs specific for ≈45 genera, with the remaining CSIs being specific for members of the orders , and , family , and some species/genera. Using this server, genome sequences were analysed for 721 strains of unknown taxonomic affiliation. Results obtained showed that 651 of these genomes contained significant numbers of CSIs specific for the following genera/families: , ’, , Cereus clade, Subtilis clade, , , , , , , , , , , , , , , , , , , , , , , and . Validity of the taxon assignment made by the server was examined by reconstructing phylogenomic trees. In these trees, all strains for which taxonomic predictions were made correctly branched with the indicated taxa. The unassigned strains likely correspond to taxa for which CSIs are lacking in our database. Results presented here show that the AppIndels server provides a useful new tool for predicting taxonomic affiliation based on shared presence of the taxon-specific CSIs. Some caveats in using this server are discussed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Borreliaceae , Caryophanaceae , conserved signature indels (CSIs) , CSIs specific for the taxa within the Bacillaceae , Legionellales and Chlorobiales , Leuconostocaceae , Neisseriales , taxonomic affiliation of uncharacterized Bacillus species and usefulness of CSIs for predicting taxonomic affiliation
Funding
This study was supported by the:
  • Natural Sciences and Engieering Research Council of Canada (Award RGPIN-2019-06397)
    • Principle Award Recipient: RadheyS. Gupta
© 2023 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.

Erratum

An erratum has been published for this content:
Corrigendum: AppIndels.com Server: A Web Based Tool for the Identification of Known Taxon-Specific Conserved Signature Indels in Genome Sequences: Validation of Its Usefulness by Predicting the Taxonomic Affiliation of >700 Unclassified strains of Species
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http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005844
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AppIndels.com server: a web-based tool for the identification of known taxon-specific conserved signature indels in genome sequences. Validation of its usefulness by predicting the taxonomic affiliation of >700 unclassified strains of Bacillus species
Int J Syst Evol Microbiol 73, 005844 (2023); https://doi.org/10.1099/ijsem.0.005844
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