InParanoid 7: new algorithms and tools for eukaryotic orthology analysis

By Gabriel Östlund, Thomas Schmitt, Kristoffer Forslund, T. Köstler, David N. Messina, Sanjit Roopra, Oliver Frings, Erik L. L. Sonnhammer. Nucleic Acids Res., 2009

674 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/06e718042aa20036fb919cb2f6c72bae7ba58a6b

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Citations in the corpus

Selecting causal genes from genome-wide association studies via functionally-coherent subnetworks (2014, methodology): “Similarity between phylogenetic profiles (downloaded from Inparanoid 45 ) were also scored using the PhenoBlast method 43 .”
Genome Sequencing and Comparative Transcriptomics of the Model Entomopathogenic Fungi Metarhizium anisopliae and M. acridum (2011, neutral): “0 [116].”
Human Ageing Genomic Resources: Integrated databases and tools for the biology and genetics of ageing (2012, background): “For example, researchers can quickly see from GenAge if homologues, from the InParanoid database (29), for a model organism gene are present in the human ageing gene set as well or if the gene is present in GenDR.”
InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic (2014, methodology): “Macaque monkey (Macaca mulatta) is still oddly placed, clearly outside the other primates, indicating that the annotation of this genome still needs to be improved (8).”
Analysis of High Accuracy, Quantitative Proteomics Data in the MaxQB Database (2012, methodology): “The locations of the genes on the chromosomes were obtained from Ensembl (19), and the ortholog pairs of proteins in different organisms were obtained from InParanoid eukaryotic ortholog database (20).”
OMA 2011: orthology inference among 1000 complete genomes (2010, background): “Most commonly, a reference splice variant is selected, usually the longest one, and used exclusively in all computations (4,13).”
Genenames.org: the HGNC resources in 2015 (2014, methodology): “HCOP currently collates orthology assertions from eggNOG (34), Ensembl Compara (2), HGNC, HomoloGene (31), InParanoid (35), OMA (36), OrthoDB (37), OrthoMCL (38), PANTHER (39), PhylomeDB (40), Treefam (41) and ZFIN (18) into a single tool, enabling comparison of these data to identify a consensus or”