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Ortholuge specifications

Information


Unique identifier OMICS_16081
Name Ortholuge
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.8
Stability Stable
Requirements
Perl, Bioperl, Phylip
Source code URL http://www.pathogenomics.ca/ortholuge/download/ortholuge-0.8.edist.tar.gz
Maintained Yes

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Maintainer


  • person_outline Debra Fulton <>

Publication for Ortholuge

Ortholuge in publications

 (9)
PMCID: 5385501
PMID: 28393877
DOI: 10.1038/srep45458

[…] proteins, predicted to function as low-permeable broad range porins or as specific transporters for yet undetermined ions, are directly regulated by nikr ( and ). comparative genomic analysis with ortholuge, a computational method that can generate precise orthologue predictions between species on a genome-wide scale, indicated that hopv and hopw are conserved in gastric helicobacter species, […]

PMCID: 5174103
PMID: 28066376
DOI: 10.3389/fmicb.2016.02056

[…] guide the assembly process for a. borkumensis sk2 (schneiker et al., ) and a. dieselolei ks 293 (liu and shao, )., genes were grouped according to orthologous clusters using the database provided by ortholuge db (whiteside et al., ). only clusters classified as supporting-species-divergence (ssd) were considered for further analyses and the rest were discarded (borderline-ssd, divergent-ssd, […]

PMCID: 4981847
PMID: 27515484
DOI: 10.1038/srep31316

[…] transcripts, constructing a map of the transcriptome, based on a previously reported transcriptome annotation., genes were grouped according to orthologous clusters using the database provided by ortholuge db. only clusters classified as supporting-species-divergence (ssd) and borderline-ssd were considered and the rest were discarded (divergent-ssd, similar non-ssd and unevaluated orthologs […]

PMCID: 4620235
PMID: 26543846
DOI: 10.1155/2015/527054

[…] was used for predicting the probable open reading frames., tentative orthologs among the three species were predicted using a transitive reciprocal best hits (rbh) approach implemented in the ortholuge pipeline [] with default settings except the e-value for blastn being set to 1e − 9. for each ortholog group, we compared each nucleotide sequence with the corresponding protein sequence […]

PMCID: 4505447
PMID: 26013493
DOI: 10.1128/JB.00330-15

[…] database () is to allow pairwise comparisons of microbial genomes and identification of orthologous genes. identification of orthologs in bacterial and archaeal genomes is also the main scope of the ortholuge database (). similarly, the atgc database () is the database of orthologous genes, but its distinctive feature is that orthologs are defined in closely related genomes, which is useful […]


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Ortholuge institution(s)
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
Ortholuge funding source(s)
Supported by the Functional Pathogenomics of Mucosal Immunity Project and Pathogenomics of Innate Immunity Project (funded by Genome Canada/Genome Prairie/Genome BC and Inimex Pharmaceuticals) and by IBM and Sun Microsystems.

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