OrthoCluster protocols

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OrthoCluster specifications

Information


Unique identifier OMICS_11720
Name OrthoCluster
Interface Web user interface
Restrictions to use None
Input data OrthoCluster receives two types of input files: the genome file and the correspondence file.
Computer skills Basic
Stability Stable
Maintained Yes

Information


Unique identifier OMICS_11720
Name OrthoCluster
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data OrthoCluster receives two types of input files: the genome file and the correspondence file.
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for OrthoCluster

OrthoCluster in pipelines

 (3)
2018
PMCID: 5807335
PMID: 29459888
DOI: 10.3389/fcimb.2018.00020

[…] number nc_024384.1) and vb_lmos_293 (genbank accession number nc_028929.1), respectively, while contig_3 contained an incomplete prophage. they are bacteriophages of the siphoviridae family orthocluster iv which have already been described as l. monocytogenes phages (denes et al., ; casey et al., ). phages from this cluster are typically between 38 and 41 kb long and have gc contents […]

2016
PMCID: 5010911
PMID: 27553646
DOI: 10.1093/gbe/evw180

[…] were made to identify contigs in at least three of the four heliconius species and not in e. isabella. a text file containing the predicted orf functional annotations (best blast hits) and orthocluster membership from each of the five trinity assemblies are available from dryad under the data identifier doi:10.5061/dryad.8d724., several assembly protocols were explored (see […]

2013
PMCID: 3629103
PMID: 23613904
DOI: 10.1371/journal.pone.0061683

[…] used to search for orthologous protein-coding genes across the four schizosaccharomyces taxa, with thresholds of e<10−10 and identity ≥0.25. then, all the possible orthologs were imported into orthocluster 2.0 to generate synteny blocks among the four organisms. the minimum orthologous gene number and the maximum mismatched gene number in each block were set to 3. only orthologous gene […]


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OrthoCluster in publications

 (17)
PMCID: 5934872
PMID: 29755580
DOI: 10.1186/s13015-018-0127-2

[…] the terms coloring and clustering will be used interchangeably. we perform our experiments on the genomes of d. melanogaster and d. yakuba which were partitioned into 64 syntenic blocks using orthocluster tool []. the dcj distance between the two genomes is 51. d. melanogaster is used as genome a with a coloring that we obtain from the hi-c data published in []. no hi-c for d. yakuba […]

PMCID: 5395790
PMID: 28420406
DOI: 10.1186/s12934-017-0680-2

[…] genetic and functional difference., because yyh13 and yyh16 were isolated from the same location, we expected their genomic structures to be highly similar. we examined synteny relationships using orthocluster based on the gene annotations and one-to-one orthologous relationships identified by inparanoid, and we found that yyh13 and yyh16 exhibited high synteny levels, whereas yyh16 and gd12 […]

PMCID: 5560861
PMID: 28726632
DOI: 10.7554/eLife.26036.043

[…] 40 eukaryotic species (excluding the low-quality gene models of pirum and abeoforma), whose genes were classified in 162,559 clusters of orthologs, 26,377 of which contained >1 gene (henceforth, ‘orthocluster’). the second database included all available unicellular holozoan genomes (i.e., six ichthyosporeans, two choanoflagellates, corallochytrium and capsaspora) and yielded 58,516 […]

PMCID: 5203792
PMID: 28040774
DOI: 10.1093/gbe/evw259

[…] ()., despite missing chromosomal segments relative to each other, the present orthologous genes are highly collinear compared with f. fujikuroi. the colinearity to f. fujikuroi, as estimated by orthocluster (), is high for all four genomes: 0.936 for f. mangiferae; 0.995 for f. proliferatum et1; 0.978 for f. proliferatum 62905, and 0.963 for f. verticillioides., genome-wide comparisons […]

PMCID: 5010911
PMID: 27553646
DOI: 10.1093/gbe/evw180

[…] contig orfs across species was performed using blast+, filtering out contigs with >99% pairwise identity. a database of cross-species sequence associations was created, with each orthocluster assigned a consensus functional description from the top uniprot blast hits. the filtering of highly similar sequences between species and the blast to the uniprot database ensured […]


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OrthoCluster institution(s)
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada

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