Bioinformatics

The Society for Archaeal Biology plays a role in collating bioinformatics resources useful for researchers engaged in archaeal research. Our collection of bioinformatics resources is meant to serve as a platform offering a list of easily accessible tools and databases useful for researchers engaged in computational analyses of archaeal genomes.

We would like to thank Dr. Stefan Schulze and Dr. Nahui Olin Medina-Chávez for their help in curating this list.

Taxonomy Database

GBIF

Archaea GBIF Backbone Taxonomy

A single, synthetic management classification with the goal of covering all archaeal names GBIF is dealing with.
NCBI Taxonomy

NCBI/Archaea taxonomy browser

Database designed for exploring the taxonomic classification of archaeal organisms.

Proteome Database

ArcPP

Archaeal Proteome Project

Combined reanalysis of archaeal proteomics datasets
ProteomeXchange

ProteomeXchange

Consortium of globally coordinated proteomics repositories.

Gene Annotation

arCOGs

arCOGs Database

The arCOGs Database is a curated database of clusters of genes within the archaeal domain that can be used for the functional annotation of genomes.
FITBAR

FITBAR: Fast Investigation Tool for Bacterial and Archaeal Regulons

Web service designed to identify new protein binding sites on fully sequenced Archaeal and Bacterial genomes.
HydDB

Hydrogenase Database

The Hydrogenase Database (HydDB) is a classification system for structural and functional analysis of hydrogenases.
KEGGs

KEGG Database

The KEGG Database is a curated database for the functional annotation of proteins based on amino acid sequence.
MCycDB

MCycDB

A curated database for comprehensively profiling methane cycling processes of environmental microbiomes.

Genome Database

BAGET 2.0

Bacterial and Archaeal Gene Exploration Tool- BAGET 2.0

A web server for the effortless retrieval of prokaryotic gene context and sequence.
GTDB

Genome Taxonomy Database

The GTDB Database is a curated database of microbial genomes with a standardised taxonomy based on phylogenetics.
HaloDom

HaloDom

A new database of halophiles across all life domains.
HaloWeb

HaloWeb

Database for complete genome sequences of Haloarchaeal microorganisms.
IMG/Archaea

IMG/Archaea

Database for analysis and annotation of archaeal genome and metagenome datasets.
MBGD

Microbial Genome Database for Comparative Analysis (MBGD)/Archaea

MBGDis a database for comparative analysis of completely sequenced microbial genomes.
GenBank

NCBI GenBank

Comprehensive database of for nucleotide sequences
UCSC

UCSC Archaeal Genome Browser

A graphical web-based resource for exploration and discovery within archaeal genomes.

Tool Database

bio.tools

bio.tools

Collection of software tools and databases in the life sciences

Protein Database

Halophile Protein Database

Halophile Protein Database

Lists the physical and chemical properties of halophilic proteins.
UniProt

UniProt

UniProt is the most comprehensive resource for information about protein sequences, their structure and function

Expression Database

GEO

NCBI Gene Expression Omnibus

Functional genomics data repository

rRNA Database

rrnDB

rrnDB

Database of variations in ribosomal RNA operons in Bacteria and Archaea
SILVA

SILVA

Database for quality checked and aligned ribosomal RNA sequence data