About
AciDB 1.0 is a database of about 600 manually curated acidophilic organisms (grow at pH <5). AciDB includes taxonomic information for each of the sequenced organisms and charts to visualize genome information and associated metadata with customizable axes. Advanced search features and general information are included, such as: genome size, G+C content, optimal pH and temperature growth of each acidophilic organism.
Features
Genomic Data of more than 590 acidophilic organisms
Navigate through all organisms by using taxonomy information. Metadata that include the full taxonomy, reported growth condition, references and direct links to the NCBI ftp site of the organism are provided.
Generate customizable scatter plots
Choose between different growth conditions and genome characteristics to customize each axis. Select genomes in the plot and get the data as a csv file containing all the genome information.
Advance search to get a curated dataset
Filter a dataset of organisms by either growth range parameters, genome metadata, taxonomic rank or all the previous conditions at the same time and download the obtained dataset complete information.
Team
AciDB was developed by the Center for Bioinformatics and Genome Biology at Fundación Ciencia & Vida.
Diego Cortez (genomic data)
David Holmes (tool conception/design)
Joaquín Jil B. (core developer)
Gonzalo Neira (tool conception/design)
Funding
This research was funded by FONDECYT 1181717 and Programa de Apoyo a Centros con Financiamiento Basal AFB170004 to Fundación Ciencia & Vida.
Cite Us
Neira, G., Cortez, D., Jil, J., Holmes, D., "AciDB 1.0: A database of acidophilic organisms, their genomic information and associated metadata" (2020)
Bioinformatics, btaa638, https://doi.org/10.1093/bioinformatics/btaa638