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InParanoid: Eukaryotic Ortholog Groups

Collection of pairwise comparisons between 100 whole genomes generated by a fully automatic method for finding orthologs and in-paralogs between TWO species. Ortholog clusters in the InParanoid are seeded with a two-way best pairwise match, after which an algorithm for adding in-paralogs is applied. The method bypasses multiple alignments and phylogenetic trees, which can be slow and error-prone steps in classical ortholog detection. Still, it robustly detects complex orthologous relationships and assigns confidence values for in-paralogs. The original data sets can be downloaded.

URL: http://inparanoid.sbc.su.se/cgi-bin/index.cgi

Resource ID: nif-0000-03024     Resource Type: Resource     Version: Latest Version

Keywords

protein, ortholog, genome, drosophila pseudoobscura, duplication, entamoeba histolytica, escherichia colik12, eukaryotic, gasterosteus aculeatus, gene, aedes aegypti, apis mellifera, bos taurus, caenorhabditis remanei, candida glabrata, canis familiaris, ciona intestinalis, cryptococcus neoformans, debaromyces hansenii, dictyostelium discoideum, genomic, homolog, inparalog, kluyveromyces lactis, macaca mulatta, monodelphis domestica, orthology, oryza sativa, outparalog, proteome, tetraodon nigroviridis, xenopus tropicalis, blast, proteome, ortholog cluster, cluster, in-paralog, paralog, automatic clustering, genome comparison

Additional Resource Types

database, data analysis service

Old URLs

http://www.cgb.ki.se/inparanoid/

Supercategory

Resource

Resource Status

Last checked up;

Abbreviation

InParanoid

Synonyms

Inparanoid eukaryotic ortholog database

Parent Organization

Curation Status

curated

Availability

Acknowledgement requested

Species

escherichia coli, anopheles gambiae, caenorhabditis briggsae, caenorhabditis elegans, drosophila melanogaster, zebrafish, takifugu rubripes, chicken, human, mouse, chimpanzee, rat, oryza sativa, plasmodium falciparum, arabidopsis thaliana, saccharomyces cerevisiae, schizosaccharomyces pombe, eukaryota

Resource PubMed IDs

PMID: 19043069, PMID: 20498707, PMID: 20883526, PMID: 21647448, PMID: 21738795, PMID: 21846611, PMID: 22465851, PMID: 22761991, PMID: 23418180, PMID: 23758924, PMID: 23922823, PMID: 24023804, PMID: 24397480, PMID: 24455408, PMID: 24604738, PMID: 24646378, PMID: 24968325, PMID: 25075304

Original Submitter

Anonymous

Version Status

Curated

Submitted On

12:00am September 21, 2010

Originated From

SciCrunch

Changes from Previous Version

First Version

Version 1

Created 4 years ago by Anonymous