ArticleNucleic acids research2015
InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 288 papers, 1 of them a synthesis that pooled it.
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288 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- OrthoXML-Tools: A Toolkit for Manipulating OrthoXML Files for Orthology Data.Journal of molecular evolution · 2025Article
- Reconstructing Evolutionary Histories with Hierarchical Orthologous Groups.Journal of molecular evolution · 2025Review
- Ten practical tips and tricks to improve the effectiveness of biological network alignment.PLoS computational biology · 2025Article
- Yellow Fever Virus Interactomes Reveal Common and Divergent Strategies of Replication and Evolution for Mosquito-borne Flaviviruses.bioRxiv : the preprint server for biology · 2025Article
- Feature Architecture-Aware Ortholog Search With fDOG Reveals the Distribution of Plant Cell Wall-Degrading Enzymes Across Life.Molecular biology and evolution · 2025Article
- Recent allopolyploidization and transcriptomic asymmetry in the mangrove shrub Acanthus tetraploideus.BMC genomics · 2025Article
- Integrating CORUM and co-fractionation mass spectrometry to create enhanced benchmarks for protein complex predictions.Briefings in bioinformatics · 2025Article
- A metric and its derived protein network for evaluation of ortholog database inconsistency.BMC bioinformatics · 2025Article
- DNA-protein quasi-mapping for rapid differential gene expression analysis in non-model organisms.BMC bioinformatics · 2024Article
- Evolutionary rate covariation is pervasive between glycosylation pathways and points to potential disease modifiers.PLoS genetics · 2024Article
- SonicParanoid2: fast, accurate, and comprehensive orthology inference with machine learning and language models.Genome biology · 2024Article
- Interrogation of RNA-protein interaction dynamics in bacterial growth.Molecular systems biology · 2024Article
- OrthoRefine: automated enhancement of prior ortholog identification via synteny.BMC bioinformatics · 2024Article
- A protein network refinement method based on module discovery and biological information.BMC bioinformatics · 2024Article
- Informatic challenges and advances in illuminating the druggable proteome.Drug discovery today · 2024Review
- Beyond blast: enabling microbiologists to better extract literature, taxonomic distributions and gene neighbourhood information for protein families.Microbial genomics · 2024Article
- Representing and extracting knowledge from single-cell data.Biophysical reviews · 2024Review
228 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
The InParanoid database (http://InParanoid.sbc.su.se) provides a user interface to orthologs inferred by the InParanoid algorithm. As there are now international efforts to curate and standardize complete proteomes, we have switched to using these resources rather than gathering and curating the proteomes ourselves. InParanoid release 8 is based on the 66 reference proteomes that the 'Quest for Orthologs' community has agreed on using, plus 207 additional proteomes from the UniProt complete proteomes--in total 273 species. These represent 246 eukaryotes, 20 bacteria and seven archaea. Compared to the previous release, this increases the number of species by 173% and the number of pairwise species comparisons by 650%. In turn, the number of ortholog groups has increased by 423%. We present the contents and usages of InParanoid 8, and a detailed analysis of how the proteome content has changed since the previous release.
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