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orthAgogue specifications

Information


Unique identifier OMICS_01691
Name orthAgogue
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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No version available

Documentation


Publication for orthAgogue

orthAgogue citations

 (19)
library_books

Comparative Genomics Highlights Symbiotic Capacities and High Metabolic Flexibility of the Marine Genus Pseudovibrio

2018
Genome Biol Evol
PMCID: 5765558
PMID: 29319806
DOI: 10.1093/gbe/evx271

[…] terms of protein diversity was analyzed and visualized in a distance tree. Therefore, to identify homologous proteins shared between the genomes, an all-against-all BLASTp was performed, after which OrthAgogue v1.0.3 () and MCL 14-137 () were used to identify orthologous groups of proteins (OGPs), where the OGPs included proteins with both orthologous and inparalogous relations. A presence/absenc […]

call_split

Genomic and phenotypic characteristics of Swedish C. jejuni water isolates

2017
PLoS One
PMCID: 5720728
PMID: 29216271
DOI: 10.1371/journal.pone.0189222
call_split See protocol

[…] uences were annotated by RAST [] and the translated coding sequences (tCDS) were extracted. To determine orthologues clusters, a reciprocal blastp query was performed using an E-value of 10−5 and the OrthAgogue [] and MCL-edge tools [].Plasmids were assembled from the raw sequence reads with Geneious de novo assembler version 8.1.9 []. […]

call_split

Signatures of adaptation and symbiosis in genomes and transcriptomes of Symbiodinium

2017
Sci Rep
PMCID: 5670126
PMID: 29101370
DOI: 10.1038/s41598-017-15029-w
call_split See protocol

[…] /current_release/knowledgebase/idmapping) and the Gene Ontology (GO) terms in UniProt-GOA release 163 (ftp.ebi.ac.uk/pub/databases/GO/goa). Proteins without functional annotation were clustered using orthAgogue v1.0.3 (e-value cut-off = 10−10) and MCL (I = 1.2, scheme 7), as recommended for extensive genetic divergence (expected among Symbiodinium clades); here we define a group of two or more suc […]

library_books

New Tools in Orthology Analysis: A Brief Review of Promising Perspectives

2017
Front Genet
PMCID: 5674930
PMID: 29163633
DOI: 10.3389/fgene.2017.00165

[…] verlap, or do not overlap, orthologous genes. It is a tool composed of several methods such as MCL, BLAST all vs. all and besides, for the identification of hypothetical orthology, OrthoVenn uses the OrthAgogue tool for identifying orthology and inparalogy relations (Wang et al., ).OrthoVenn is available on web server and it allows personalized protein analysis from defined species on the part of […]

call_split

Whole genome based phylogeny of reptile associated Helicobacter indicates independent niche adaptation followed by diversification in a poikilothermic host

2017
Sci Rep
PMCID: 5566214
PMID: 28827684
DOI: 10.1038/s41598-017-09091-7
call_split See protocol

[…] l BLAST was performed for all predicted proteins of the whole genomes (Table ) at an E-value cutoff of 1E-6. To determine the orthologous relationships of all proteins, the BLAST output was parsed by Orthagogue using default settings. To determine the orthologous groups, Markov clustering (MCL) was performed using MCL-edge. Genes encoding the proteins were aligned with each other within their resp […]

call_split

Protein domain architectures provide a fast, efficient and scalable alternative to sequence based methods for comparative functional genomics

2017
F1000Res
PMCID: 5031134
PMID: 27703668
DOI: 10.5256/f1000research.10140.r15679
call_split See protocol

[…] protein sequences containing at least one protein domain signature were considered for analysis. BBH were obtained using Blastp (2.2.28+) with an E-value cutoff of 10 −5 and -max_target_seqs of 10 5. OrthaGogue (1.0.3) combined with MCL (14-137) was used to identify protein clusters on the base of sequence similarity. […]

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orthAgogue institution(s)
Semantic Systems Biology Group, Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway

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