Inparanoid: a comprehensive database of eukaryotic orthologs

By Kevin P. O'Brien, Maido Remm, Erik L. L. Sonnhammer. Nucleic Acids Res., 2004

791 citations recorded by the source corpus.

The Inparanoid eukaryotic ortholog database (http://inparanoid.cgb.ki.se/) is a collection of pairwise ortholog groups between 17 whole genomes; Anopheles gambiae, Caenorhabditis briggsae, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Takifugu rubripes, Gallus gallus, Homo sapiens, Mus musculus, Pan troglodytes, Rattus norvegicus, Oryza sativa, Plasmodium falciparum, Arabidopsis thaliana, Escherichia coli, Saccharomyces cerevisiae and Schizosaccharomyces pombe. Complete proteomes for these genomes were derived from Ensembl and UniProt and compared pairwise using Blast, followed by a clustering step using the Inparanoid program. An Inparanoid cluster is seeded by a reciprocally best-matching ortholog pair, around which inparalogs (should they exist) are gathered independently, while outparalogs are excluded. The ortholog clusters can be searched on the website using Ensembl gene/protein or UniProt identifiers, annotation text or by Blast alignment against our protein datasets. The entire dataset can be downloaded, as can the Inparanoid program itself.

Subfields: Molecular Biology, Pharmacology

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Citations in the corpus

Orthologs, Paralogs, and Evolutionary Genomics 1 (2005, methodology): “Bets and then incorporating additional inparalogs according to developed statistical criteria (67, 82).”
Widespread Protein Aggregation as an Inherent Part of Aging in C. elegans (2010, methodology): “orthologs using the Inparanoid eukaryotic ortholog database version 7.0”
Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood Topology (2007, methodology): “Instead, for each choice of α, we compared the resulting node mappings to sequence-based ortholog predictions from the Inparanoid database [21] and chose the α (= 0.”
TreeFam: 2008 Update (2007, methodology): “Tree-based inference of orthologues is more robust to rate diﬀerences than BLAST -based orthologue inference, which has been used in other databases such as InParanoid (5), KOGs (6), HomoloGene (7) and OrthoMCL-DB (8).”
Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. (2008, background): “Convergent restoration of some genes to singleton status after multiple rounds of duplication in independent lineages suggests that there may be selective advantages for the organism to have only single copies of these genes (Paterson et al. 2006).”
An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man (vol 140, pg 744, 2010) (2010, positive): “For each human TF, we used the InParanoid algorithm (O’Brien et al., 2005) to identify its set of amino-acid sequence orthologs in mouse.”
eggNOG: automated construction and annotation of orthologous groups of genes (2007, methodology): “Numerous methods have been developed to derive orthologs and orthologous groups, ranging from the simple reciprocal-best-hit approach, via InParanoid (5), MultiParanoid (6), identiﬁcation best-hit triangles (2,7,8) and clustering-based approaches (9), to tree-based meth-ods (10–13).”
ChemProt: a disease chemical biology database (2010, methodology): “Data are transferred between organisms by using the Inparanoid orthology database (44).”
TreeFam: a curated database of phylogenetic trees of animal gene families (2005, methodology): “In this way, ortholog inference in TreeFam is different from that used by most other ortholog databases such as Inparanoid ( 2 ), Ensembl-Compara (3), KOGs (4), OrthoMCL (5) and HomoloGene (6).”