Proteinortho pipeline

Proteinortho specifications

Information


Unique identifier OMICS_05355
Name Proteinortho
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 Proteinortho

Proteinortho IN pipelines

 (8)
2017
PMCID: 5346208
PMID: 28284195
DOI: 10.1186/s12866-017-0965-y

[…] of all annotated protein coding sequences in a. baumannii strains atcc 17978, atcc 19606t, d1279779, sdf, acicu, ab0057, wm99c and 6870155, and acinetobacter baylyi adp1 were executed through the proteinortho tool [52] to identify putative orthologous/paralogous proteins in each of the strains. transport protein predictions were made using the transporter automated annotation pipeline […]

2017
PMCID: 5573122
PMID: 28846714
DOI: 10.1371/journal.pone.0183567

[…] c. truncatum had more homologues in fusarium species, specifically in f. oxysporum than in any other fungus outside the genus colletotrichum. orthologue analysis of colletotrichum genus using proteinortho showed that 88.8% of the c. truncatum genes (12,186) had an orthologue in at least one of the ten colletotrichum species. there were 6,081 orthogroups consisting of proteins […]

2016
PMCID: 4810266
PMID: 26978387
DOI: 10.3390/v8030076

[…] to detect distant relationships with proteins available in the ncbi nr database [36]., the genome synteny between the brmv and other marseilleviruses was checked using the mauve program [37]. the proteinortho tool [38] was used to define the strict core of bona fide orthologs shared among brmv and amoebal marseilleviruses from lineages a–c, using the reciprocal best hit strategy with 10−5, […]

2016
PMCID: 4986183
PMID: 27527502
DOI: 10.1186/s12864-016-2974-x

[…] supercontigs., the phylogenetic tree of a. westerdijkiae and the other eight aspergillus species was constructed using whole genome-wide sequences. orthologous protein prediction was performed using proteinortho (v5.11, with default parameters, except that identity = 75) [87]. among the predicted orthologous gene clusters, 561 highly conserved single-copy gene clusters were chosen and aligned […]

2015
PMCID: 4304616
PMID: 25600302
DOI: 10.1186/s13071-014-0622-3

[…] investigation (additional file 1)., the sequencing and assembly of the g. tigrina transcriptome allows for an important genetic comparison between this free-living worm and its pathogenic relatives. proteinortho [34] was used to identify orthologous protein sequence groups shared between and among g. tigrina and the parasitic species schistosoma mansoni and echinococcosis multilocularis. […]

Proteinortho institution(s)
RNA Bioinformatics Group, Department of Pharmaceutical Chemistry, Philipps-University Marburg, Germany

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