ArticleNucleic acids research2010
InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 357 papers.
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357 citing papers in PubMed.
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- Identifying essential proteins from protein-protein interaction networks based on influence maximization.BMC bioinformatics · 2022Article
- Evolutionary analyses of genes in Echinodermata offer insights towards the origin of metazoan phyla.Genomics · 2022Article
- InParanoid-DIAMOND: faster orthology analysis with the InParanoid algorithm.Bioinformatics (Oxford, England) · 2022Article
- Data-driven identification of inherent features of eukaryotic stress-responsive genes.NAR genomics and bioinformatics · 2022Article
- Prediction of disease-associated nsSNPs by integrating multi-scale ResNet models with deep feature fusion.Briefings in bioinformatics · 2022Article
- Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms.Nucleic acids research · 2022Article
- How to Use the Candida Genome Database.Methods in molecular biology (Clifton, N.J.) · 2022Article
- A disease-related essential protein prediction model based on the transfer neural network.Frontiers in genetics · 2022Article
- Cross-Species Analysis Reveals Co-Expressed Genes Regulating Antler Development in Cervidae.Frontiers in genetics · 2022Article
297 more citing papers are in PubMed but not listed here.
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8 authors.
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Abstract
The InParanoid project gathers proteomes of completely sequenced eukaryotic species plus Escherichia coli and calculates pairwise ortholog relationships among them. The new release 7.0 of the database has grown by an order of magnitude over the previous version and now includes 100 species and their collective 1.3 million proteins organized into 42.7 million pairwise ortholog groups. The InParanoid algorithm itself has been revised and is now both more specific and sensitive. Based on results from our recent benchmarking of low-complexity filters in homology assignment, a two-pass BLAST approach was developed that makes use of high-precision compositional score matrix adjustment, but avoids the alignment truncation that sometimes follows. We have also updated the InParanoid web site (http://InParanoid.sbc.su.se). Several features have been added, the response times have been improved and the site now sports a new, clearer look. As the number of ortholog databases has grown, it has become difficult to compare among these resources due to a lack of standardized source data and incompatible representations of ortholog relationships. To facilitate data exchange and comparisons among ortholog databases, we have developed and are making available two XML schemas: SeqXML for the input sequences and OrthoXML for the output ortholog clusters.
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