orthAgogue protocols

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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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Publication for orthAgogue

orthAgogue in pipelines

 (7)
2018
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. […]

2017
PMCID: 5293770
PMID: 28224116
DOI: 10.3389/fcimb.2017.00031

[…] (wolf and koonin, ) was performed of the mycoplasma proteins using an e-value cut-off of 1e−05 and a maximum target sequence of 105. the blast file created was used to find orthologous proteins with orthagogue (ekseth et al., ) excluding protein pairs with an overlap below 50%. clustering of orthologous proteins was done using mcl (enright et al., ) setting 1.5 as main inflation. with a sparql […]

2017
PMCID: 5309974
PMID: 28289537
DOI: 10.1186/s13578-017-0138-6

[…] hapla [], bursaphelenchus xylophilus [], caenorhabditis elegans [], pristionchus pacifics [] and ascaris suum [] genomes and h. avenae transcriptomes, orthologous families were constructed by orthagogue [] (default parameters) and mcl [] (i = 1.5). the 703 single-copy ortholog families of all 8 nematodes were subjected to multiple global alignment by musle [] and trimming by trimai []. […]

2016
PMCID: 5037721
PMID: 27598122
DOI: 10.3390/ijms17091442

[…] families were constructed for predicted proteins of meloidogyne enterolobii, meloidogyne hapla, meloidogyne incognita, bursaphelenchus xylophilus, globodera pallida and caenorhabditis elegans by orthagogue [] at the default setting. protein multiple alignments were carried out using muscle [] for each of 1022 single-copy ortholog families extracted from the orthagogue result. the resulting […]

2016
PMCID: 5037721
PMID: 27598122
DOI: 10.3390/ijms17091442

[…] and caenorhabditis elegans by orthagogue [] at the default setting. protein multiple alignments were carried out using muscle [] for each of 1022 single-copy ortholog families extracted from the orthagogue result. the resulting alignments were concatenated into one combined alignment. poorly-aligned regions were removed by trimal []. the phylogenomic tree was inferred by mega6 [] using […]


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orthAgogue in publications

 (15)
PMCID: 5720728
PMID: 29216271
DOI: 10.1371/journal.pone.0189222

[…] 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 []., the lipooligosaccharide (los) locus class was determined […]

PMCID: 5670126
PMID: 29101370
DOI: 10.1038/s41598-017-15029-w

[…] group (ko-hog) as those proteins for which the uniprot top match(es) have the same assigned ko term. we clustered proteins that show no significant (e ≤ 10−10) match against any uniprot entry using orthagogue and mcl, and define each of the resulting groups as an orthagogue-mcl homolog group (om-hog)., the 228,391 proteins with uniprot matches were grouped into 40,688 up-hogs (mean size 3.85, […]

PMCID: 5566214
PMID: 28827684
DOI: 10.1038/s41598-017-09091-7

[…] 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 […]

PMCID: 5031134
PMID: 27703668
DOI: 10.5256/f1000research.10140.r15679

[…] 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., domain architecture based clusters were built by clustering proteins […]

PMCID: 5430854
PMID: 28455506
DOI: 10.1038/s41598-017-01133-4

[…] of cog classes was assessed using a fisher exact test with q-value multiple testing correction., protein sequences of c. jejuni m1cam, 11168 and 81–176 were clustered into putative hgs with orthagogue. for this, a collective database was generated and proteins of each strain were queried against this database. the reciprocal best-hit protein pairs were identified by applying an e-value […]


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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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