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Gene orthology databases | Comparative genomics

Orthology, refining the concept of homology, is the cornerstone of evolutionary comparative studies. With the ever-increasing availability of genomic data, inference of orthology has become instrumental for generating hypotheses about gene functions…
COGs
Dataset

COGs the Clusters of Orthologous Groups of proteins

Provides clusters of orthologous groups (COGs) and updated annotation of those…

Provides clusters of orthologous groups (COGs) and updated annotation of those COGs. COGs is a database where organisms are sorted according to the NCBI Taxonomy database. Each gene entry in a COG is…

OrthoDB
Dataset

OrthoDB

Provides orthologs, genes inherited by extant species from a single gene in…

Provides orthologs, genes inherited by extant species from a single gene in their last common ancestor. OrthoDB includes a total of 5756 species, providing ortholog groups for the clades of: 3663…

eggNOG
Dataset

eggNOG evolutionary genealogy of genes: Non-supervised Orthologous Groups

Provides orthologous groups (OGs) of proteins at different taxonomic levels,…

Provides orthologous groups (OGs) of proteins at different taxonomic levels, each with integrated and summarized functional annotations. Developments since the latest public release include changes…

NCBI HomoloGene
Dataset

NCBI HomoloGene

An automated system for constucting putative homology groups from the complete…

An automated system for constucting putative homology groups from the complete genes sets of a wide range of eukaryotic species.

HieranoiDB
Dataset

HieranoiDB

An online database for hierarchical groups of orthologs inferred by the…

An online database for hierarchical groups of orthologs inferred by the Hieranoid algorithm. HieranoiDB with a web interface makes it easy to search and visualize the output of Hieranoid, and to…

MicrobesOnline
Dataset

MicrobesOnline

Includes over 1000 complete genomes of bacteria, archaea and fungi and…

Includes over 1000 complete genomes of bacteria, archaea and fungi and thousands of expression microarrays from diverse organisms. To assist in annotating genes and in reconstructing their…

pVOGs
Dataset

pVOGs prokaryotic Virus Orthologous Groups

Represents a comprehensive set of orthologous gene families shared across…

Represents a comprehensive set of orthologous gene families shared across multiple complete genomes of viruses that infect bacterial or archaeal hosts. The uses of pVOGs include functional annotation…

Evola
Dataset

Evola Database of Evolutionary Features of Human Genes

Provides orthology information about originally annotated human genes in the…

Provides orthology information about originally annotated human genes in the H-Invitational database (H-InvDB). Evola contains two datasets (i) a comprehensive set of orthologs and (ii) more reliable…

OPTIC
Dataset

OPTIC Orthologous and Paralogous TranscrIpts in Clades

Provides sets of gene predictions and orthologous groups for six clades. OPTIC…

Provides sets of gene predictions and orthologous groups for six clades. OPTIC is designed to provide pre-calculated phylogenetic datasets that are benefit to clade genomic analyses. A useful feature…

InParanoid
Dataset

InParanoid

Developed to address the need to identify orthologs. InParanoid uses the…

Developed to address the need to identify orthologs. InParanoid uses the pairwise similarity scores, calculated using NCBI-Blast, between two complete proteomes for constructing orthology groups. An…

MBGD
Dataset

MBGD Microbial Genome Database

A comprehensive ortholog database for flexible comparative analysis of…

A comprehensive ortholog database for flexible comparative analysis of microbial genomes, where the users are allowed to create an ortholog table among any specified set of organisms. The MyMBGD…

FLAGdb++
Dataset

FLAGdb++

Helps biologists to find the flanking insertion sites (FSTs) that interrupt the…

Helps biologists to find the flanking insertion sites (FSTs) that interrupt the genes in which they are interested. The FLAGdb information system was developed with the aim of using whole plant…

PLAZA
Dataset

PLAZA

Makes comparative genomics data for plants available through a user-friendly…

Makes comparative genomics data for plants available through a user-friendly web interface. Structural and functional annotation, gene families, protein domains, phylogenetic trees and detailed…

OrthoDisease
Dataset

OrthoDisease

Provides a database of human disease orthologs. OrthoDisease contains 2935…

Provides a database of human disease orthologs. OrthoDisease contains 2935 distinct human disease phenotypes from OMIM, mapped to 2313 out of 21 673 human genes and their orthologs in 99 other…

OrthoMCL-DB
Dataset

OrthoMCL-DB

Contains ortholog groups for most completely sequenced and annotated eukaryotes…

Contains ortholog groups for most completely sequenced and annotated eukaryotes for a number of completely sequenced and annotated prokaryotes. OrthoMCL-DB provides a wealth of functionality,…

PhylomeDB
Dataset

PhylomeDB

Gives access to catalogues of gene phylogenies (phylomes). PhylomeDB provides…

Gives access to catalogues of gene phylogenies (phylomes). PhylomeDB provides alignments and trees enriched with relevant annotations, as well as prediction of orthology and paralogy relationships,…

TreeFam
Dataset

TreeFam

Stores phylogenetic trees inferred from animal genomes. TreeFam is a database…

Stores phylogenetic trees inferred from animal genomes. TreeFam is a database that aims at providing comprehensive gene evolution information and orthology assignments for animal gene families. The…

EchinoDB
Dataset

EchinoDB

A repository of orthologous transcripts from echinoderms that is searchable via…

A repository of orthologous transcripts from echinoderms that is searchable via keywords and sequence similarity. From transcripts we identified 749,397 clusters of orthologous loci. We have…

PhyloFacts
Dataset

PhyloFacts

A structural phylogenomic encyclopedia containing almost 10,000…

A structural phylogenomic encyclopedia containing almost 10,000 'books' for protein families and domains, with pre-calculated structural, functional and evolutionary analyses. PhyloFacts…

QuartetS-DB
Dataset

QuartetS-DB

Orthology predictions among 1621 complete genomes (1365 bacterial, 92 archaeal,…

Orthology predictions among 1621 complete genomes (1365 bacterial, 92 archaeal, and 164 eukaryotic), covering >7 million proteins and 4 million pairwise orthologs.

Ensembl Compara
Dataset

Ensembl Compara

Provides cross-species resources and analyses, at both the sequence level and…

Provides cross-species resources and analyses, at both the sequence level and the gene level. Data can be accessed using the Compara Perl API, BioMart, or comparative genomics pages on the browser.…

MetaPhOrs
Dataset

MetaPhOrs

A public repository of phylogeny-based orthologs and paralogs that were…

A public repository of phylogeny-based orthologs and paralogs that were computed using phylogenetic trees available in twelve public repositories.

OrtholugeDB
Dataset

OrtholugeDB

Contains Ortholuge-based orthology predictions for completely sequenced…

Contains Ortholuge-based orthology predictions for completely sequenced bacterial and archaeal genomes.

HCOP
Dataset

HCOP HGNC Comparison of Orthology Predictions

Provides a useful method to integrate, compare and access a variety of…

Provides a useful method to integrate, compare and access a variety of disparate sources of human orthology data.

PGDBj
Dataset

PGDBj Plant Genome DataBase Japan

Aims to integrate plant genome-related information from databases (DBs) and the…

Aims to integrate plant genome-related information from databases (DBs) and the literature. The PGDBj is comprised of three component DBs and a cross-search engine, which provides a seamless search…

VOCS
Desktop

VOCS Viral Orthologous Clusters

Searches and extracts genome, gene and protein data from the Viral…

Searches and extracts genome, gene and protein data from the Viral Bioinformatics Resource Center (VBRC) database. VOCS includes Asfarviridae, Baculoviridae, Iridoviridae, and Poxviridae. It compares…

FUNGIpath
Dataset

FUNGIpath

A tool built using a two-stage approach. Groups of orthologous proteins…

A tool built using a two-stage approach. Groups of orthologous proteins predicted using complementary methods of detection were collected in a relational database. Each group was further mapped on to…

BRAD
Dataset

BRAD BRAssica Database

A database for Brassica crops at the whole genome scale. BRAD provides several…

A database for Brassica crops at the whole genome scale. BRAD provides several datasets, like the complete Brassica A genome sequence from Brassica rapa (B. rapa), coming from de novo assembly of…

P-POD
Dataset

P-POD Princeton Protein Orthology Database

Offers a simple way to visualize and analyze the relationships between…

Offers a simple way to visualize and analyze the relationships between homologous proteins in order to infer function.

HOGENOM
Dataset

HOGENOM

A database of homologous genes from fully sequenced organisms (bacteria,…

A database of homologous genes from fully sequenced organisms (bacteria, archeaea and eukarya), structured under ACNUC sequence database management system.

HOMOLENS
Dataset

HOMOLENS

A database of homologous genes from Ensembl organisms and Ensembl families,…

A database of homologous genes from Ensembl organisms and Ensembl families, structured under ACNUC sequence database management system.

HOVERGEN
Dataset

HOVERGEN

A database of homologous vertebrate genes, structured under ACNUC sequence…

A database of homologous vertebrate genes, structured under ACNUC sequence database management system.

OGO
Dataset

OGO

Allows users to retrieve integrated results when querying orthology…

Allows users to retrieve integrated results when querying orthology information, providing a gene product-oriented output instead of a traditional information resource-oriented one.

Gclust Server
Dataset

Gclust Server

Makes clusters of protein sequences from predicted protein sequences in a…

Makes clusters of protein sequences from predicted protein sequences in a selected set of genomes. Gclust Server is a comparative genomic database for phylogenetic profiling based on pre-calculated…

Metazome
Dataset

Metazome

Gathers the proteomes, organized into gene families, of several metazoans.

Gathers the proteomes, organized into gene families, of several metazoans.

KOG
Dataset

KOG EuKaryotic Orthologous Groups

Allows identification of ortholog and paralog proteins. KOG is a database using…

Allows identification of ortholog and paralog proteins. KOG is a database using euKaryotic Orthologous Groups from NCBI, that gives access to classifications, eukaryotic orthologous groups (KOGs) and…

GOOD
Dataset

GOOD Gene-Oriented Ortholog Database

Employs genomic locations of transcripts to cluster alternative…

Employs genomic locations of transcripts to cluster alternative splicing-derived isoforms prior to ortholog delineation to eliminate the interference from AS.

KO
Dataset

KO KEGG Orthology

Stores molecular-level functions associated with ortholog groups. KO is a…

Stores molecular-level functions associated with ortholog groups. KO is a database in which knowledge of molecular-level functions is organized with the concept of functional orthologs. Higher-level…

POGs/PlantRBP
Dataset

POGs/PlantRBP

Allows cross-species comparisons among the major model plant species…

Allows cross-species comparisons among the major model plant species Arabidopsis thaliana (Arabidopsis), Oryza sativa (rice) and Zea mays (maize). POGs/PlantRBP is a database that clusters proteins…

EPGD
Dataset

EPGD Eukaryotic Paralog Group Database

Allows users to find information about paralogous genes. EPGD focuses on…

Allows users to find information about paralogous genes. EPGD focuses on families of paralogs and integrates spatial and temporal data to diagnose gene duplication processes. In this database, about…

Roundup
Dataset

Roundup

A comprehensive database of gene orthologs for over 1800 genomes, including…

A comprehensive database of gene orthologs for over 1800 genomes, including eukaryota, bacteria, archaea and viruses. Orthologs are inferred using the reciprocal smallest distance algorithm. Roundup…

ProGMap
Dataset

ProGMap Protein Group Mappings

A web-tool designed to help researchers and database annotators to assess the…

A web-tool designed to help researchers and database annotators to assess the coherence of protein groups defined in various databases and thereby facilitate the annotation of newly sequenced…

YOGY
Dataset

YOGY

A web-based resource for retrieving orthologous proteins from ten eukaryotic…

A web-based resource for retrieving orthologous proteins from ten eukaryotic organisms and one prokaryote.

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