AciDB 1.0: a database of acidophilic organisms, their genomic information and associated metadata

Gonzalo Neira; Diego Cortez; Joaquin Jil; David S Holmes

doi:10.1093/bioinformatics/btaa638

AciDB 1.0: a database of acidophilic organisms, their genomic information and associated metadata

Bioinformatics. 2020 Dec 8;36(19):4970-4971. doi: 10.1093/bioinformatics/btaa638.

Authors

Gonzalo Neira¹, Diego Cortez¹, Joaquin Jil¹, David S Holmes^{1

2

3}

Affiliations

¹ Center for Bioinformatics and Genome Biology, Fundación Ciencia & Vida, Santiago, Chile.
² Universidad San Sebastián, Santiago, Chile.
³ Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile.

PMID: 32702093
DOI: 10.1093/bioinformatics/btaa638

Abstract

Motivation: There are about 600 available genome sequences of acidophilic organisms (grow at a pH < 5) from the three domains of the Tree of Life. Information about acidophiles is scattered over many heterogeneous sites making it extraordinarily difficult to link physiological traits with genomic data. We were motivated to generate a curated, searchable database to address this problem.

Results: AciDB 1.0 is a curated database of sequenced acidophiles that enables researchers to execute complex queries linking genomic features to growth data, environmental descriptions and taxonomic information.

Availability and implementation: AciDB 1.0 is freely available online at: http://AciDB.cl. The source code is released under an MIT license at: https://gitlab.com/Hawkline451/acidb/.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Databases, Factual
Genome
Genomics*
Metadata*
Software