title: Seqenv: linking sequences to environments through text mining.
abstract: Understanding the distribution of taxa and associated traits across different environments is one of the central questions in microbial ecology. High-throughput sequencing (HTS) studies are presently generating huge volumes of data to address this biogeographical topic. However, these studies are often focused on specific environment types or processes leading to the production of individual, unconnected datasets. The large amounts of legacy sequence data with associated metadata that exist can be harnessed to better place the genetic information found in these surveys into a wider environmental context. Here we introduce a software program, seqenv, to carry out precisely such a task. It automatically performs similarity searches of short sequences against the "nt" nucleotide database provided by NCBI and, out of every hit, extracts-if it is available-the textual metadata field. After collecting all the isolation sources from all the search results, we run a text mining algorithm to identify and parse words that are associated with the Environmental Ontology (EnvO) controlled vocabulary. This, in turn, enables us to determine both in which environments individual sequences or taxa have previously been observed and, by weighted summation of those results, to summarize complete samples. We present two demonstrative applications of seqenv to a survey of ammonia oxidizing archaea as well as to a plankton paleome dataset from the Black Sea. These demonstrate the ability of the tool to reveal novel patterns in HTS and its utility in the fields of environmental source tracking, paleontology, and studies of microbial biogeography. To install seqenv, go to: https://github.com/xapple/seqenv.
authors.affiliation: Department of Ecology and Genetics, Limnology, Uppsala University, Uppsala, Sweden.
authors.forename: Lucas
authors.initials: L
authors.lastname: Sinclair
authors.affiliation: Infrastructure and Environment Research Division, School of Engineering, University of Glasgow, Glasgow, United Kingdom.
authors.forename: Umer Z
authors.initials: UZ
authors.lastname: Ijaz
authors.affiliation: The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Lars Juhl
authors.initials: LJ
authors.lastname: Jensen
authors.affiliation: Western Australia Organic and Isotope Geochemistry Centre (WA-OIGC), Department of Chemistry, Curtin University of Technology, Bentley, WA, Australia.
authors.forename: Marco J L
authors.initials: MJL
authors.lastname: Coolen
authors.affiliation: Institute of Biological & Environmental Sciences, University of Aberdeen, Aberdeen, United Kingdom.
authors.forename: Cecile
authors.initials: C
authors.lastname: Gubry-Rangin
authors.affiliation: Institute of Soil Biology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.
authors.forename: Alica
authors.initials: A
authors.lastname: Chroňáková
authors.affiliation: Bioinformatics Group, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.|Institute of Marine Biology Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion Crete, Greece.
authors.forename: Anastasis
authors.initials: A
authors.lastname: Oulas
authors.affiliation: Institute of Marine Biology Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion Crete, Greece.
authors.forename: Christina
authors.initials: C
authors.lastname: Pavloudi
authors.affiliation: Department of Molecular Ecology, Microbial Genomics and Bioinformatics Group, Max Planck Institute for Marine Microbiology, Bremen, Germany.
authors.forename: Julia
authors.initials: J
authors.lastname: Schnetzer
authors.affiliation: Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.
authors.forename: Aaron
authors.initials: A
authors.lastname: Weimann
authors.affiliation: Hawkesbury Institute for the Environment, University of Western Sydney, Hawkesbury, Sydney, Australia.
authors.forename: Ali
authors.initials: A
authors.lastname: Ijaz
authors.affiliation: Department of Ecology and Genetics, Limnology, Uppsala University, Uppsala, Sweden.
authors.forename: Alexander
authors.initials: A
authors.lastname: Eiler
authors.affiliation: Warwick Medical School, University of Warwick, Warwick, United Kingdom.
authors.forename: Christopher
authors.initials: C
authors.lastname: Quince
authors.affiliation: Institute of Marine Biology Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Heraklion Crete, Greece.
authors.forename: Evangelos
authors.initials: E
authors.lastname: Pafilis
keywords: Bioinformatics; Ecology; Genomics; Microbiology; Open source software; Pipeline; Sequence analysis; Statistics; Text processing