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OrthologTables

Each file represents orthology predictions made for a query protein by multiple orthology algorithms. Tables are created by searching for a gene within ortholog lists, and listing genes named as orthologs to it according to each database.

Each row is a putative ortholog, and contains Uniprot Accession, Uniprot Entry, Ensmebl proteins ID, species, count of algorithms prediction orthology, and individual algorithm predictions.

Note on naming: Since most protein IDs were given in uniprot format, I converted the minority ensembl proteins IDs to uniprot where possible. In these cases, both the ensemble ID and uniprot ID are kept, but no effort was made to convert uniprot IDs into Ensembl.

Common Name Uniprot ID
Anopheles gambiae (Mosquito) ANOGA
Aquifex aeolicus AQUAE
Arabidopsis Thaliana ARATH
Neosartorya fumigata (Black mold) ASPFU
Bacillus subtilis BACSU
Bacteroides thetaiotaomicron BACTN
Bos taurus (Cattle) BOVIN
Bradyrhizobium diazoefficiens BRADU
Branchiostoma floridae (Lancelet) BRAFL
Caenorhabditis elegans (Worm) CAEEL
Candida albicans CANAL
Canis lupus familiaris (Dog) CANFA
Chlamydia trachomatis CHLTR
Chloroflexus aurantiacus CHLAA
Gallus gallus (Chicken) CHICK
Ciona intestinalis (Tunicate) CIOIN
Cryptococcus neoformans CRYNJ
Danio rerio (Zebrafish) DANRE
Deinococcus radiodurans DEIRA
Dictyoglomus turgidum DICTD
Dictyosteium discoideum DICTI
Drosophila melanogaster (Fly) DROME
Escherichia coli ECOLI
Fusobacterium nucleatum FUSNN
Geobacter sulfurreducens GEOSL
Giardia intestinalis GIAIC
Gloeobacter violaceus GLOVI
Halobacterium salinarum HALSA
Homo sapiens (Human) HUMAN
Ixodes scapularis (Tick) IXOSC
Korarchaeum cryptofilum KORCO
Leishmania major LEIMA
Leptospira interrogans LEPIN
Macaca mulatta (Rhesus macaque) MACMU
Methanocaldococcus jannaschii METJA
Methanosarcina acetivorans METAC
Monosiga brevicollis (Choanoflagellate) MONBE
Monodelphis domestica (Opossum) MONDO
Mus musculus (Mouse) MOUSE
Mycobacterium tuberculosis MYCTU
Nematostella vectensis (Sea anemone) NEMVE
Neurospora crassa (Bread mold) NEUCR
Ornithorhynchus anatinus (Platypus) ORNAN
Pan troglodytes (Chimp) PANTR
Phaeosphaeria nodorum PHANO
Physcomitrella patens PHYPA
Plasmodium falciparum PLAF7
Pseudomonas aeruginosa PSEAE
Rattus rattus (Rat) RAT
Rhodopirellula baltica RHOBA
Saccaromyces cerevisiae (Budding yeast) YEAST
Schistosoma mansoni (Blood fluke) SCHMA
Schizosaccharomyces pombe (Fission yeast) SCHPO
Sclerotinia sclerotiorum SCLS1
Streptomyces coelicolor STRCO
Sulfolobus solfataricus SULSO
Synechocystis sp. SYNY3
Takifugu rubripes (Pufferfish) TAKRU
Thermococcus kodakaraensis THAPS
Thermodesulfovibrio yellowstonii THEKO
Thermotoga maritima THEYD
Trichomonas vaginalis TRIVA
Ustilago maydis (Corn smut/Huitlacoche USTMA
Xenopus tropicalis (Frog) XENTR
Yarrowia lipolytica YARLI

Ortholog groups are pulled from the Quest for Orthologs reference proteome benchmarking 2011. The following algorithms ortholog calling algorithms were run on identical proteome sets covering 66 species, including eukaryotes, archaea and bacteria. http://www.ebi.ac.uk/reference_proteomes

Hieranoid 2.0 (KO) release 74

EnsemblCompara v2

InParanoid

InParanoidCore

metaPhOrs missing genomes: {PYRKO,STRCO,THEMA}

OMA Groups (RefSet5)

OMA OMA Pairs (Refset5)

orthoinspector 1.30

PANTHER 8.0 (all)

PANTHER 8.0 (LDO only)

phylomeDB

RBH - 26 genomes missing

RSD 0.8 1e-5 Deluca (Roundup)

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