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Thursday, December 2 • 9:55am - 10:05am
OP 02 - ProTaxa: software to easily perform phylogenomic analyses for prokaryotic taxa

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ProTaxa: software to easily perform phylogenomic analyses for prokaryotic taxa

Presenting Author: Joseph Wirth, Harvey Mudd College

Eliot Bush, Harvey Mudd College

Abstract:The nucleotide sequences of 16S ribosomal RNA (rRNA) genes have been used to inform the taxonomic placement of prokaryotes for several decades, but recent research has demonstrated that whole-genome approaches can better resolve the evolutionary relationships of organisms, especially when taxa are closely-related. However, the vast number of publicly available 16S rRNA gene sequences make this gene useful for obtaining a rough estimate of the phylogeny for a given taxon. Unfortunately, the reliance of 16S rRNA as the sole phylogenetic marker often causes closely-related organisms to be omitted from taxonomic analyses. In addition, NCBI Taxonomy is not an authoritative database for prokaryotic taxonomy. Although it is roughly accurate, the database has many erroneous entries, especially when it comes to the accurate designation of type material. While there are existing tools available to facilitate taxonomic placement, the genome-selection methods leave much to be desired. For example, the TYpe strain Genome Server (TYGS) uses a proprietary genome database, and the Microbial Genome Atlas (MiGA) relies on relationships provided by NCBI's Taxonomy database. ProTaxa was developed to resolve these issues in a freely accessible (open source) way. NCBI's Taxonomy database is cross-referenced with the List of Prokaryotes with Standing in Nomenclature (LPSN), a more definitive resource for prokaryotic taxonomy, which allows easy linking to NCBI’s sequence databases. This software also employs a unique strategy to identify closely-related genomes that were omitted by identifying and utilizing phylogenetic markers specific to the input genome. These approaches greatly improve taxonomic placements and are largely automated.


Joseph Wirth

Postdoctoral Scholar in Interdisciplinary Computation, Harvey Mudd College
I am a microbiologist and only recently began learning computational biology. I am interested in the ecology, evolution, and physiology of microbes, especially those organisms that are environmentally or clinically relevant. I seek to apply a combination of genetic, biochemical, physiological... Read More →

Thursday December 2, 2021 9:55am - 10:05am MST
Ballroom Salon 1