PhyloFunDB: A Pipeline to Create and Update Functional Gene Taxonomic Databases

Ohana Y A Costa; Mattias de Hollander; Eiko E Kuramae; Paul L E Bodelier

doi:10.3390/microorganisms10061093

PhyloFunDB: A Pipeline to Create and Update Functional Gene Taxonomic Databases

Microorganisms. 2022 May 25;10(6):1093. doi: 10.3390/microorganisms10061093.

Authors

Ohana Y A Costa¹, Mattias de Hollander^{1

2}, Eiko E Kuramae^{1

3}, Paul L E Bodelier¹

Affiliations

¹ Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands.
² Department of Terrestrial Ecology Bioinformatics Unit, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands.
³ Ecology and Biodiversity Group, Department of Biology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.

Abstract

The increase in sequencing capacity has amplified the number of taxonomically unclassified sequences in most databases. The classification of such sequences demands phylogenetic tree construction and comparison to currently classified sequences, a process that demands the processing of large amounts of data and use of several different software. Here, we present PhyloFunDB, a pipeline for extracting, processing, and inferring phylogenetic trees from specific functional genes. The goal of our work is to decrease processing time and facilitate the grouping of sequences that can be used for improved taxonomic classification of functional gene datasets.

Keywords: functional genes; pipeline; taxonomy.

Grants and funding

This research received no external funding.