DIOPT Documentation

DIOPT Version 9

Website: DIOPT version 9

About DIOPT

The identification of orthologs is commonly used for bioinformatics activities such as data mining and establishing models for human diseases. Moreover, our group notes that researchers analyzing the results of screens performed at the Drosophila RNAi Screening Center (DRSC) frequently wish to identify mammalian orthologs of the fly genes that were "hits" (positive results) in their screens.

In helping DRSC screeners to identify orthologs using existing tools and algorithms, we recognized a need for a user-friendly approach to viewing and comparing ortholog predictions obtained using different tools and algorithms. This was our motivation in developing DIOPT. To facilitate identification of orthologs specifically of human disease-associated genes, we further developed DIOPT-DIST. Information about our approaches to development of both tools is summarized below.

The DIOPT Approach

Many tools have emerged to meet the need to identify orthologs. However, low coverage and heterogeneity of these tools present an obstacle to scientists who want to identify a one or a few highest-confidence orthologs for a given gene of interest or conversely, want to cast a wide net and follow up on all possible orthologs of a gene.

Our goal is to provide an easy-to-use resource that facilitates summary, comparison and access to various sources of ortholog predictions. DIOPT integrates human, mouse, fly, worm, zebrafish and yeast ortholog predictions made by Ensembl Compara, HomoloGene, Inparanoid, Isobase, OMA, orthoMCL, Phylome, RoundUp, and TreeFam. DIOPT lets users find ortholog pairs for a specified gene or genes identified by one, many or all of these published approaches. This provides a streamlined method for integration, comparison and access to orthology predictions originating from algorithms based on sequence homology, phylogenetic trees, and functional similarity. DIOPT calculates a simple score indicating the number of tools that support a given orthologous gene-pair relationship, as well as a weighted score based on functional assessment using high quality GO molecular function annotation of all fly-human orthologous pairs predicted by each tool. Differences in the algorithms used by each tool to predict orthologous relationship is one source of difference in the set of predictions made by one tool versus another. However, we also note that some of these differences might be attributable to use of different genome annotation releases used by some tools versus others, and that not all tools cover all of the species that we include in the DIOPT tool (see Tables 1,2 and 3).

DIOPT also displays protein and domain alignments, including percent amino acid identity, for predicted ortholog pairs. These should help you to identify the most appropriate matches among multiple possible orthologs.

The following summary figures and tables help to explain our approach and summarize the tools and algorithms included in DIOPT.

DIOPT integration schema

 

Summary Information and Publications for the Tools Integrated in

Table 1: Summary Information and Publications for the Tools Integrated in DIOPT

Prediction Method Source Prediction Algorithm Coverage PMID
Compara Ensembl Phylogenetic approach 228 species (vs 104) 19029536
Homologene NCBI Combination of BBH*, tree and synteny 21 species (vs. 68) 11125071
Inparanoid Stockholm University, Sweden BBH* approach to identify orthologs and in-paralogs 273 species (vs. 8) 11743721
25429972
Isobase MIT Sequence and PPI* network alignments 5 species (vs.2, Nov. 2014) 21177658
OMA CBRG, ETH Zurich BBH*, global sequence alignments QFO2020 17545180
OrthoDB University of Geneva Phylogenetic approach >7302 species (vs.10.1) 20972218
25428351
orthoMCL University of Pennsylvania Markov Cluster algorithm 605 species (vs. 6.6) 12952885
Phylome Centre for Genomic Regulation (CRG), Spain Reconstruction of evolutionary histories of all genes in a genome, also known as phylome. 1059 species,120 Phylomes (vs. 4) QFO2014 17962297
24275491
RoundUp Harvard Medical School RSD*, modified BBH* 2044 species (Apr 2013) 16777906
TreeFam Wellcome Trust Sanger Institute Manually curated based on trees 109 species (vs. 9) 16381935
24194607
Panther University of Southern California Phylogenetic approach 132 species (vs. 16.1) 26578592
HGNC European Bioinformatics Institute (EMBL-EBI) Manually curated 3 species (Aug 2021)  
ZFIN Zebrafish Model Organism Database Sequence similarity analysis and manual curation 4 species (July 2021)  
Domainoid Stockholm University,Sweden Infer orthology on the domain level QFO2020 31660857
eggNOG Embl, Germany Graph-based algorithms 5090 species (vs. 5.0) 26582926
OrthoFinder University of Oxford Graph-based algorithms Run code with 12 ref proteome (2020) 26578592
OrthoInspector Institut de Génétique et de Biologie Moléculaire et Cellulaire A novel orthogroup inference algorithm that solves a previously undetected gene length bias in orthogroup inference, resulting in significant improvements in accuracy. QFO 2020 21219603
Hieranoid Stockholm Bioinformatics Center The OrthoInspector algorithm is divided into three main steps. First, the results of a Blast all-versus-all (proteomes are blasted against each other) is provided by the user and is parsed to find all the Blast best hits for each protein and to create the groups of inparalogs. Second, the inparalog groups for each organism are compared in a pairwise fashion to define potential orthologs and/or in-paralogs. Third, best hits that contradict the potential orthology between entities are detected. QFO 2020 27742821
ECGA ECOCYC Genome Database Collection Manually curated 2 species (Feb 2021) NA
SGD Saccharomyces Genome Database Manually curated 1 species of paralogs (Oct 2020) NA
sonicParanoid University of Tokyo Graph-based algorithms Run code with 12 ref proteome (2020) 30032301
NCBI NIH Details are not published. Combination of BBH, tree and synteny. Human2Vertebrate  
SwiftOrtho Iowa State University Iowa State University NA 31648300

  BBH, Best Blast Hits
  RSD, Reciprocal Smallest Distance
  PPI, Protein-Protein Interactions

Genome Release Information

Table 2A: Genome Release Information for the Tools Integrated in DIOPT (Version 9)

  Worm Fish Fly Human Mouse Yeast Fission Yeast Frog Rat Thale cress Mosquito E coli
Compara WBcel235 GRCz11 BDGP6.32 GRCh38 GRCm39 R64-1-1 NA Xenopus_tropicalis_v9.1 Rnor_6.0 NA NA NA
Domainoid ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020
ECGA NA NA NA ECGA Feb 2021 NA NA NA NA NA NA NA ECGA Feb 2021
eggNOG WormBase Ensembl FlyBase Ensembl Ensembl SGD PomBase Ensembl Ensembl Araport VectorBase Ecocyc
HGNC NA NA NA HGNC Aug 2021 HGNC Aug 2021 NA NA NA HGNC Aug 2021 NA NA NA
Hieranoid ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020
Homologene WS195 Zv9 FlyBase r5.48 GRCh38 GRCm38.p2 R64-1-1 ASM294v2 Xtropicalis_v7 Rnor_5.0 TAIR10 AgamP3.3 NA
Inparanoid ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020
Isobase Ensembl v59 NA Ensembl v59 Ensembl v59 Ensembl v59 Ensembl v59 NA NA NA NA NA NA
OMA ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020
orthoDB Refseq Refseq FlyBase Refseq Refseq NA NA Refseq Refseq Refseq VectorBase NA
OrthoFinder ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020
OrthoInspector ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020
orthoMCL ref proteome 2020 ref proteome 2020 ref proteome 2020 HostDB HostDB FungiDB FungiDB ref proteome 2020 ref proteome 2020 ref proteome 2020 VectorBase ref proteome 2020
Panther ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020
Phylome ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020
RoundUp UniProt Apr 2013 UniProt Apr 2013 UniProt Apr 2013 UniProt Apr 2013 UniProt Apr 2013 UniProt Apr 2013 UniProt Apr 2013 UniProt Apr 2013 NA NA NA NA
SGD NA NA NA NA NA SGD Oct 2020 NA NA NA NA NA NA
sonicParanoid ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020
TreeFam Ensembl v69 Ensembl v69 Ensembl v69 Ensembl v69 Ensembl v69 Ensembl v69 Ensembl v69 Ensembl v69 Ensembl v69 NA VectorBase NA
ZFIN NA ZFIN Aug 2021 ZFIN Aug 2021 ZFIN Aug 2021 ZFIN Aug 2021 NA NA NA NA NA NA NA
NCBI NA EntrezGene Oct 2021 NA EntrezGene Oct 2021 EntrezGene Oct 2021 NA NA EntrezGene Oct 2021 EntrezGene Oct 2021 NA NA NA
SwiftOrtho ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020 ref proteome 2020

 

Table 2B: Additional Information About Genome Releases (Version 9)

Other Resource Version
WormBase release280
FlyBase release6.40
RefSeq release207 (July 2021)
EntrezGene 26-July-2021

Table 3. Maximum DIOPT score for each orthologous relationship

(version 9)

 

Orthologous Relationship Max score Type Relevant Tools
bacteria-baker's yeast 12 ortholog eggNOG; Panther; orthoMCL; Hieranoid; OMA; Phylome; sonicParanoid; Inparanoid; OrthoFinder; SwiftOrtho; OrthoInspector; Domainoid;
bacteria-fish 12 ortholog Panther; SwiftOrtho; Phylome; Domainoid; sonicParanoid; orthoMCL; Hieranoid; OMA; OrthoFinder; eggNOG; OrthoInspector; Inparanoid;
bacteria-fission yeast 12 ortholog OrthoInspector; Domainoid; OMA; OrthoFinder; Inparanoid; Hieranoid; SwiftOrtho; eggNOG; orthoMCL; Panther; sonicParanoid; Phylome;
bacteria-fly 12 ortholog OMA; sonicParanoid; OrthoInspector; Domainoid; OrthoFinder; Inparanoid; orthoMCL; SwiftOrtho; eggNOG; Hieranoid; Panther; Phylome;
bacteria-frog 11 ortholog SwiftOrtho; sonicParanoid; OrthoFinder; Domainoid; OrthoInspector; Hieranoid; Panther; Phylome; OMA; eggNOG; Inparanoid;
bacteria-human 13 ortholog orthoMCL; Panther; OrthoFinder; Phylome; Domainoid; Inparanoid; SwiftOrtho; ECGA; OrthoInspector; eggNOG; Hieranoid; sonicParanoid; OMA;
bacteria-mosquito 11 ortholog OrthoInspector; Inparanoid; SwiftOrtho; Panther; Domainoid; Phylome; OMA; OrthoFinder; Hieranoid; eggNOG; sonicParanoid;
bacteria-mouse 12 ortholog Domainoid; eggNOG; OMA; sonicParanoid; Hieranoid; Panther; Phylome; Inparanoid; SwiftOrtho; orthoMCL; OrthoFinder; OrthoInspector;
bacteria-rat 12 ortholog Hieranoid; OrthoInspector; OMA; orthoMCL; Inparanoid; SwiftOrtho; Domainoid; Panther; sonicParanoid; Phylome; eggNOG; OrthoFinder;
bacteria-thale cress 12 ortholog OrthoInspector; Hieranoid; Inparanoid; sonicParanoid; Panther; SwiftOrtho; Phylome; eggNOG; OMA; Domainoid; OrthoFinder; orthoMCL;
bacteria-worm 12 ortholog OrthoFinder; Panther; Phylome; OrthoInspector; orthoMCL; sonicParanoid; Inparanoid; Domainoid; SwiftOrtho; OMA; eggNOG; Hieranoid;
baker's yeast-fish 16 ortholog SwiftOrtho; sonicParanoid; orthoMCL; OMA; Domainoid; Panther; Hieranoid; Phylome; RoundUp; OrthoFinder; TreeFam; eggNOG; OrthoInspector; Homologene; Compara; Inparanoid;
baker's yeast-fission yeast 14 ortholog OMA; OrthoInspector; Homologene; Domainoid; Panther; Inparanoid; Phylome; OrthoFinder; orthoMCL; RoundUp; sonicParanoid; TreeFam; eggNOG; Hieranoid;
baker's yeast-fly 16 ortholog OrthoInspector; Isobase; orthoMCL; Homologene; Panther; Phylome; Inparanoid; RoundUp; OrthoFinder; Domainoid; TreeFam; OMA; Compara; eggNOG; sonicParanoid; Hieranoid;
baker's yeast-frog 15 ortholog SwiftOrtho; OrthoFinder; Panther; Phylome; RoundUp; TreeFam; OrthoInspector; Domainoid; Compara; OMA; sonicParanoid; Homologene; Hieranoid; Inparanoid; eggNOG;
baker's yeast-human 17 ortholog Compara; OrthoFinder; Homologene; sonicParanoid; Inparanoid; OMA; SwiftOrtho; Isobase; OrthoInspector; Domainoid; Panther; Phylome; eggNOG; RoundUp; orthoMCL; TreeFam; Hieranoid;
baker's yeast-mosquito 12 ortholog Phylome; Homologene; TreeFam; OrthoInspector; Inparanoid; OMA; Domainoid; sonicParanoid; OrthoFinder; eggNOG; Hieranoid; Panther;
baker's yeast-mouse 17 ortholog Domainoid; orthoMCL; Isobase; OrthoFinder; Panther; OrthoInspector; Phylome; sonicParanoid; OMA; RoundUp; Hieranoid; TreeFam; Compara; eggNOG; Homologene; Inparanoid; SwiftOrtho;
baker's yeast-rat 15 ortholog Hieranoid; OrthoFinder; OMA; eggNOG; Homologene; Panther; Inparanoid; OrthoInspector; orthoMCL; Domainoid; Phylome; SwiftOrtho; TreeFam; sonicParanoid; Compara;
baker's yeast-thale cress 14 ortholog Panther; OrthoFinder; sonicParanoid; Domainoid; Phylome; TreeFam; OrthoInspector; Homologene; OMA; Inparanoid; Hieranoid; SwiftOrtho; eggNOG; orthoMCL;
baker's yeast-worm 17 ortholog Compara; eggNOG; Hieranoid; OrthoFinder; sonicParanoid; orthoMCL; OrthoInspector; Homologene; Isobase; OMA; Inparanoid; SwiftOrtho; Panther; Phylome; Domainoid; RoundUp; TreeFam;
fish-fission yeast 15 ortholog sonicParanoid; Panther; Phylome; RoundUp; OrthoFinder; TreeFam; OMA; orthoMCL; Homologene; Domainoid; Inparanoid; SwiftOrtho; eggNOG; Hieranoid; OrthoInspector;
fish-fly 18 ortholog ZFIN; Hieranoid; Panther; OMA; Phylome; sonicParanoid; RoundUp; orthoMCL; TreeFam; OrthoFinder; Compara; Homologene; Inparanoid; SwiftOrtho; Domainoid; eggNOG; OrthoInspector; OrthoDB;
fish-frog 16 ortholog OrthoFinder; OMA; Phylome; SwiftOrtho; RoundUp; sonicParanoid; TreeFam; Compara; OrthoInspector; Domainoid; OrthoDB; Homologene; eggNOG; Panther; Hieranoid; Inparanoid;
fish-human 19 ortholog Hieranoid; NCBI; ZFIN; OrthoDB; OrthoInspector; Panther; Phylome; Homologene; RoundUp; TreeFam; Inparanoid; Compara; SwiftOrtho; Domainoid; orthoMCL; eggNOG; sonicParanoid; OMA; OrthoFinder;
fish-mosquito 14 ortholog sonicParanoid; Homologene; Inparanoid; SwiftOrtho; OrthoDB; OrthoFinder; Panther; Phylome; Domainoid; TreeFam; OMA; eggNOG; OrthoInspector; Hieranoid;
fish-mouse 18 ortholog sonicParanoid; ZFIN; Panther; Domainoid; Phylome; orthoMCL; RoundUp; TreeFam; eggNOG; OrthoInspector; Compara; Homologene; Hieranoid; Inparanoid; SwiftOrtho; OMA; OrthoFinder; OrthoDB;
fish-rat 16 ortholog Hieranoid; eggNOG; Homologene; OrthoDB; Inparanoid; SwiftOrtho; Panther; sonicParanoid; Phylome; TreeFam; OrthoInspector; orthoMCL; Domainoid; Compara; OrthoFinder; OMA;
fish-thale cress 15 ortholog Domainoid; Homologene; Inparanoid; sonicParanoid; OrthoDB; Hieranoid; SwiftOrtho; eggNOG; orthoMCL; Panther; OMA; OrthoFinder; Phylome; TreeFam; OrthoInspector;
fish-worm 17 ortholog OMA; orthoMCL; OrthoDB; OrthoInspector; Hieranoid; Panther; Phylome; RoundUp; TreeFam; Homologene; Compara; sonicParanoid; Inparanoid; SwiftOrtho; OrthoFinder; Domainoid; eggNOG;
fission yeast-fly 14 ortholog Domainoid; sonicParanoid; Homologene; Hieranoid; Inparanoid; OMA; eggNOG; Panther; Phylome; RoundUp; TreeFam; orthoMCL; OrthoInspector; OrthoFinder;
fission yeast-frog 14 ortholog OrthoInspector; OMA; Hieranoid; Panther; Phylome; RoundUp; TreeFam; OrthoFinder; Homologene; Inparanoid; eggNOG; SwiftOrtho; sonicParanoid; Domainoid;
fission yeast-human 15 ortholog Domainoid; OMA; Homologene; orthoMCL; Inparanoid; OrthoInspector; Hieranoid; SwiftOrtho; OrthoFinder; eggNOG; sonicParanoid; Panther; Phylome; RoundUp; TreeFam;
fission yeast-mosquito 12 ortholog Panther; OMA; OrthoFinder; Phylome; TreeFam; Hieranoid; eggNOG; OrthoInspector; sonicParanoid; Homologene; Inparanoid; Domainoid;
fission yeast-mouse 15 ortholog Inparanoid; SwiftOrtho; Hieranoid; orthoMCL; Panther; Phylome; eggNOG; RoundUp; TreeFam; OMA; OrthoInspector; Domainoid; OrthoFinder; Homologene; sonicParanoid;
fission yeast-rat 14 ortholog Panther; SwiftOrtho; orthoMCL; Phylome; OrthoInspector; TreeFam; sonicParanoid; Domainoid; eggNOG; Hieranoid; Homologene; OrthoFinder; OMA; Inparanoid;
fission yeast-thale cress 14 ortholog Homologene; Panther; orthoMCL; Inparanoid; Phylome; SwiftOrtho; sonicParanoid; TreeFam; OrthoFinder; eggNOG; Domainoid; Hieranoid; OrthoInspector; OMA;
fission yeast-worm 15 ortholog OrthoInspector; Domainoid; OMA; Homologene; Inparanoid; sonicParanoid; SwiftOrtho; OrthoFinder; Hieranoid; orthoMCL; eggNOG; Panther; Phylome; RoundUp; TreeFam;
fly-frog 16 ortholog OMA; OrthoDB; Hieranoid; Panther; Phylome; RoundUp; OrthoFinder; TreeFam; Compara; sonicParanoid; eggNOG; Homologene; OrthoInspector; Inparanoid; Domainoid; SwiftOrtho;
fly-human 19 ortholog Domainoid; Hieranoid; Homologene; OrthoFinder; orthoMCL; sonicParanoid; Inparanoid; OrthoDB; SwiftOrtho; Isobase; eggNOG; Panther; Phylome; RoundUp; TreeFam; OrthoInspector; User_Submission; Compara; OMA;
fly-mosquito 13 ortholog Homologene; TreeFam; Inparanoid; Hieranoid; OrthoInspector; eggNOG; sonicParanoid; OrthoDB; OMA; Panther; OrthoFinder; Phylome; Domainoid;
fly-mouse 18 ortholog Domainoid; Compara; OrthoInspector; OrthoFinder; Hieranoid; orthoMCL; sonicParanoid; eggNOG; OrthoDB; Isobase; Homologene; Panther; Phylome; Inparanoid; OMA; RoundUp; TreeFam; SwiftOrtho;
fly-rat 16 ortholog Hieranoid; OrthoDB; orthoMCL; sonicParanoid; OMA; Panther; Phylome; OrthoFinder; TreeFam; eggNOG; Compara; OrthoInspector; Homologene; Domainoid; Inparanoid; SwiftOrtho;
fly-thale cress 15 ortholog Panther; sonicParanoid; Phylome; OrthoFinder; TreeFam; Homologene; Inparanoid; orthoMCL; SwiftOrtho; eggNOG; OrthoInspector; Domainoid; OMA; Hieranoid; OrthoDB;
fly-worm 18 ortholog OMA; Domainoid; sonicParanoid; OrthoFinder; Homologene; OrthoDB; Hieranoid; Isobase; Inparanoid; Panther; SwiftOrtho; OrthoInspector; Phylome; RoundUp; eggNOG; TreeFam; orthoMCL; Compara;
frog-human 17 ortholog Compara; NCBI; eggNOG; Domainoid; Homologene; Inparanoid; OrthoDB; Hieranoid; SwiftOrtho; OrthoFinder; Panther; OMA; sonicParanoid; Phylome; OrthoInspector; RoundUp; TreeFam;
frog-mosquito 14 ortholog Panther; sonicParanoid; Phylome; TreeFam; Homologene; OrthoFinder; Inparanoid; Domainoid; eggNOG; OrthoInspector; SwiftOrtho; Hieranoid; OMA; OrthoDB;
frog-mouse 16 ortholog OrthoInspector; Homologene; Domainoid; Inparanoid; SwiftOrtho; Hieranoid; OrthoDB; sonicParanoid; OrthoFinder; Panther; eggNOG; Phylome; RoundUp; TreeFam; OMA; Compara;
frog-rat 15 ortholog OMA; Homologene; sonicParanoid; Panther; Inparanoid; Hieranoid; Phylome; SwiftOrtho; TreeFam; OrthoInspector; Compara; eggNOG; OrthoFinder; Domainoid; OrthoDB;
frog-thale cress 14 ortholog Panther; eggNOG; Hieranoid; Phylome; TreeFam; Homologene; OrthoInspector; sonicParanoid; Inparanoid; OrthoFinder; SwiftOrtho; OMA; Domainoid; OrthoDB;
frog-worm 16 ortholog Compara; eggNOG; Domainoid; OrthoDB; Homologene; sonicParanoid; OrthoInspector; OrthoFinder; Inparanoid; Panther; SwiftOrtho; Phylome; OMA; Hieranoid; RoundUp; TreeFam;
human-mosquito 14 ortholog Phylome; TreeFam; Homologene; eggNOG; OMA; Inparanoid; Domainoid; SwiftOrtho; OrthoFinder; OrthoInspector; Hieranoid; OrthoDB; Panther; sonicParanoid;
human-mouse 20 ortholog OrthoInspector; OrthoDB; Domainoid; Isobase; OrthoFinder; Panther; Homologene; Phylome; HGNC; RoundUp; Inparanoid; NCBI; TreeFam; Hieranoid; SwiftOrtho; eggNOG; Compara; sonicParanoid; OMA; orthoMCL;
human-rat 18 ortholog OMA; Compara; Hieranoid; Homologene; OrthoFinder; sonicParanoid; HGNC; NCBI; Inparanoid; orthoMCL; SwiftOrtho; eggNOG; OrthoInspector; OrthoDB; Panther; Phylome; Domainoid; TreeFam;
human-thale cress 15 ortholog Panther; eggNOG; Phylome; TreeFam; OMA; Hieranoid; sonicParanoid; Homologene; Inparanoid; SwiftOrtho; OrthoInspector; OrthoFinder; OrthoDB; Domainoid; orthoMCL;
human-worm 18 ortholog OrthoFinder; Hieranoid; Compara; OrthoInspector; orthoMCL; eggNOG; OMA; sonicParanoid; OrthoDB; Isobase; Domainoid; Panther; Homologene; Phylome; Inparanoid; RoundUp; TreeFam; SwiftOrtho;
mosquito-mouse 14 ortholog OrthoDB; OrthoFinder; Homologene; Domainoid; Panther; OrthoInspector; Inparanoid; Phylome; SwiftOrtho; TreeFam; eggNOG; OMA; Hieranoid; sonicParanoid;
mosquito-rat 14 ortholog OrthoInspector; Panther; OMA; Phylome; TreeFam; Domainoid; Homologene; sonicParanoid; OrthoFinder; Inparanoid; Hieranoid; SwiftOrtho; eggNOG; OrthoDB;
mosquito-thale cress 14 ortholog SwiftOrtho; OrthoDB; Panther; sonicParanoid; Phylome; Domainoid; OMA; TreeFam; eggNOG; Hieranoid; Homologene; OrthoInspector; Inparanoid; OrthoFinder;
mosquito-worm 14 ortholog eggNOG; Phylome; Homologene; TreeFam; OrthoInspector; Domainoid; OrthoFinder; Inparanoid; SwiftOrtho; Hieranoid; sonicParanoid; OMA; OrthoDB; Panther;
mouse-rat 16 ortholog Compara; OMA; OrthoFinder; Homologene; Domainoid; Inparanoid; OrthoInspector; SwiftOrtho; eggNOG; OrthoDB; sonicParanoid; orthoMCL; Hieranoid; Panther; Phylome; TreeFam;
mouse-thale cress 15 ortholog eggNOG; OrthoInspector; Inparanoid; Panther; Domainoid; SwiftOrtho; Phylome; OMA; TreeFam; sonicParanoid; Hieranoid; OrthoFinder; orthoMCL; Homologene; OrthoDB;
mouse-worm 18 ortholog OrthoFinder; TreeFam; Compara; Homologene; Hieranoid; OrthoInspector; Inparanoid; eggNOG; SwiftOrtho; orthoMCL; OMA; sonicParanoid; OrthoDB; Isobase; Panther; Domainoid; Phylome; RoundUp;
rat-thale cress 15 ortholog eggNOG; Phylome; TreeFam; Homologene; OrthoFinder; Inparanoid; OrthoInspector; SwiftOrtho; orthoMCL; sonicParanoid; Domainoid; OMA; OrthoDB; Hieranoid; Panther;
rat-worm 16 ortholog OMA; Domainoid; eggNOG; Homologene; OrthoFinder; OrthoDB; OrthoInspector; Inparanoid; SwiftOrtho; Hieranoid; sonicParanoid; Panther; Phylome; TreeFam; Compara; orthoMCL;
thale cress-worm 15 ortholog Phylome; orthoMCL; TreeFam; Homologene; sonicParanoid; Domainoid; eggNOG; Inparanoid; SwiftOrtho; OMA; OrthoFinder; OrthoInspector; Hieranoid; OrthoDB; Panther;
bacteria-bacteria 11 paralog Inparanoid; SwiftOrtho; Panther; orthoMCL; Phylome; sonicParanoid; Domainoid; OrthoFinder; OMA; OrthoInspector; eggNOG;
baker's yeast-baker's yeast 15 paralog Compara; Domainoid; eggNOG; sonicParanoid; Homologene; Isobase; Inparanoid; Panther; Phylome; OrthoInspector; OrthoFinder; RoundUp; OMA; SGD; orthoMCL;
fish-fish 15 paralog Inparanoid; OrthoDB; SwiftOrtho; orthoMCL; Panther; Phylome; RoundUp; OrthoFinder; Domainoid; sonicParanoid; Compara; OrthoInspector; OMA; eggNOG; Homologene;
fission yeast-fission yeast 12 paralog Homologene; Inparanoid; Panther; eggNOG; Phylome; OMA; RoundUp; OrthoInspector; sonicParanoid; OrthoFinder; Domainoid; orthoMCL;
fly-fly 15 paralog Domainoid; OMA; OrthoDB; Isobase; Homologene; Panther; OrthoInspector; Phylome; Inparanoid; RoundUp; eggNOG; Compara; OrthoFinder; sonicParanoid; orthoMCL;
frog-frog 14 paralog Inparanoid; sonicParanoid; SwiftOrtho; OrthoDB; Domainoid; Panther; Phylome; eggNOG; RoundUp; Compara; OrthoFinder; OrthoInspector; OMA; Homologene;
human-human 16 paralog Compara; OrthoFinder; orthoMCL; OrthoInspector; eggNOG; OMA; Domainoid; OrthoDB; Homologene; Isobase; Inparanoid; Panther; sonicParanoid; SwiftOrtho; Phylome; RoundUp;
mosquito-mosquito 11 paralog Panther; Phylome; OMA; Homologene; OrthoFinder; Inparanoid; OrthoInspector; eggNOG; sonicParanoid; Domainoid; OrthoDB;
mouse-mouse 17 paralog OrthoInspector; OrthoFinder; sonicParanoid; orthoMCL; OrthoDB; Isobase; Panther; HGNC; Homologene; Phylome; RoundUp; Inparanoid; SwiftOrtho; Compara; Domainoid; eggNOG; OMA;
rat-rat 15 paralog orthoMCL; OrthoDB; HGNC; OrthoFinder; Panther; Phylome; eggNOG; Compara; Domainoid; OrthoInspector; OMA; Homologene; sonicParanoid; Inparanoid; SwiftOrtho;
thale cress-thale cress 13 paralog Inparanoid; sonicParanoid; SwiftOrtho; OrthoDB; OMA; OrthoInspector; Panther; OrthoFinder; Phylome; Domainoid; orthoMCL; eggNOG; Homologene;
worm-worm 16 paralog Homologene; Inparanoid; OrthoInspector; SwiftOrtho; orthoMCL; OrthoDB; Isobase; eggNOG; Domainoid; Panther; sonicParanoid; Phylome; RoundUp; OrthoFinder; Compara; OMA;

Table 4. DIOPT Weights

DIOPT weights were calculated based on the mean semantic similarity of high quality GO molecular function annotation of all fly-human orthologous pairs predicted by each tool from DIOPT vs1. As such, they do not predict overall performance of an algorithm. Please go to the DIOPT publication for detailed information (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-357).

Prediction Method DIOPT Weight
Compara 0.93
Domainoid 1
ECGA 1.5
eggNOG 0.9
HGNC 1.5
Hieranoid 1
Homologene 1
Inparanoid 1.05
Isobase 0.95
OMA 1.01
OrthoDB 1.01
OrthoFinder 1
OrthoInspector 1
orthoMCL 0.9
Panther 1.1
Phylome 0.91
RoundUp 1.03
SGD 1.5
sonicParanoid 1
TreeFam 0.96
ZFIN 1.5
NCBI 1
SwiftOrtho 1

DIOPT Score Distributions

Ortholog Score Distribution (version 9)

DIOPT 9 ortholog distribution graph

Paralog Score Distribution (version 9)

DIOPT 9 paralog distribution graph

 

 

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Diopt Versions

9.1 Oct 2021

  • added 2 prediction algorithms (NCBI, Domainoid)

9.0 Sept 2021 -

  • added 2 species: Mosquito (Anopheles gambiae) and E. coli
  • added 2 sources of annotation (SGD and ECOCYC)
  • added 2 prediction algorithms (sonicParanoid and Domainoid)

 

8.5- Aug 2021 -

  • updated UI

8.0- Aug 2019 -

7.1- Mar 2018 -

  •  Allow user to submit missing relationships
  •  Allow user to add feedback

7.0- Jan 2018 -

  • Updated Data Sources
  • added 3 new algorithms: OrthoFinder, OrthoInspector, Hieranoid as a sources
  • added new species: Arabidopsis (Thale Cress)

6.0- Dec 2016 -

  • Updated Data Sources
  • added eggNOG as a source
  • Added paralogs

5.5- Oct 2016 - Added multi-sequence alignment from target "All" heatmap

5.4- Sept 2016 - Added target species "All" and new filter

 

5.3- May 2016 - Added more prediction tools (Panther, HGNC and ZFIN)
5.2.1- April 2016 - Added orthologous rank
High: best score both ways AND DIOPT score >=2
Moderate:
(best score forward or reverse) AND DIOPT score >=2
DIOPT score >=4
Low: all others
5.2- April 2016 - Added New Spcecies (Rattus norvegicus)
5.1.1 - December 2015 - Added Best forward and reverse columns
5.1 - November 2015 - Upgraded gene matching algorithm
5.0 - November 2015 - Upgraded data sources to version 5