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Protocols

InParanoid specifications

Information


Unique identifier OMICS_05350
Name InParanoid
Restrictions to use None
Version 8.0
Maintained Yes

Maintainer


  • person_outline Erik Sonnhammer

Publications for InParanoid

InParanoid citations

 (217)
library_books

Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota

2018
BMC Genomics
PMCID: 5937819
PMID: 29690866
DOI: 10.1186/s12864-018-4683-0

[…] Pairwise orthologous groups between two species were identified using InParanoid 8 []. We identified 160 sets of 1:1 orthologous protein groups from 71 Ascomycota species and a Basidiomycota species Ustilago maydis, which was used as an outgroup (Additional file : Table […]

library_books

Environmental adaptation of Acanthamoeba castellanii and Entamoeba histolytica at genome level as seen by comparative genomic analysis

2018
PMCID: 5859476
PMID: 29559848
DOI: 10.7150/ijbs.23869

[…] roteins and aminoacyl-tRNA synthetases. The Eh genome harbors more than twice as many copies for ribosomal protein genes than the Ac genome: 213 versus 86 genes (Table , Supplementary). Consistently, InParanoid tool identified 64 orthology groups including 62 ribosomal proteins from Ac, and 141 from Eh. Table compares the number of the multi-copy ribosomal protein genes between Ac and Eh. We have […]

library_books

A multi omics study of the grapevine downy mildew (Plasmopara viticola) pathosystem unveils a complex protein coding and noncoding based arms race during infection

2018
Sci Rep
PMCID: 5768699
PMID: 29335535
DOI: 10.1038/s41598-018-19158-8

[…] The ortholog groups from the 15 oomycete species including P. viticola were used to identify the oomycete core genome. Pairs of genomes were compared using Inparanoid and the outputs were integrated using QuickParanoid (http://pl.postech.ac.kr/QuickParanoid/). Phylogenetic analyses of the oomycete dataset were performed using a concatenation of 312 core […]

call_split

Phylogenomic Perspective on the Relationships and Evolutionary History of the Major Otocephalan Lineages

2018
Sci Rep
PMCID: 5760653
PMID: 29317769
DOI: 10.1038/s41598-017-18432-5
call_split See protocol

[…] t be affected by misleading history signals, such as ‘hidden paralogs’, we generated 8-species-genome COGs (core-ortholog groups) that were used to search potential orthologs instead of the universal InParanoid database. The HaMStR pipeline was performed for orthology assignment. Fish-specific genome duplication in teleosts, which may result in “one-to-two” or “one-to-many” rather than “one-to-one […]

library_books

Adaptation of Arabidopsis thaliana to the Yangtze River basin

2017
Genome Biol
PMCID: 5745794
PMID: 29284515
DOI: 10.1186/s13059-017-1378-9

[…] s), Arabidopsis lyrata (MN47) [], and Capsella rubella (MTE) [], was constructed, with MN47 and MTE as the outgroups. Orthologous genes among A. thaliana, A. lyrata, and C. rubella were identified by InParanoid [] with default parameters. Nucleotide diversity π, Watterson’s estimator θ, and F ST were calculated in a 200-kb sliding window with a step size of 10 kb. […]

library_books

FunCoup 4: new species, data, and visualization

2017
Nucleic Acids Res
PMCID: 5755233
PMID: 29165593
DOI: 10.1093/nar/gkx1138

[…] hared transcription factor binding (TFB), and genetic interaction profile similarity (GIN). FunCoup relies on transfer of orthology information between the included proteomes, using the comprehensive InParanoid () database, to increase the quality and the coverage of the inference of functional association between genes/proteins. FunCoup employs unique scoring functions for each type of data (e.g. […]

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InParanoid institution(s)
Stockholm Bioinformatics Center, Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Solna, Sweden

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