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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 citations

 (213)
library_books

Comparative Genomics and Mutational Analysis Reveals a Novel XoxF Utilizing Methylotroph in the Roseobacter Group Isolated From the Marine Environment

2018
Front Microbiol
PMCID: 5934484
PMID: 29755426
DOI: 10.3389/fmicb.2018.00766

[…] arcula bermudensis HTCC2503 as the outgroup) consisting of 219 gene products with a combined length of 95,680 amino acid residues was determined using the bidirectional BLAST+ approach implemented in proteinortho5 (), excluding all genes with duplicates in any comparison genome. After alignment with muscle (), the gene products were concatenated and unalignable regions were filtered out using gblo […]

library_books

Parallel evolution of Batesian mimicry supergene in two Papilio butterflies, P. polytes and P. memnon

2018
Sci Adv
PMCID: 5906075
PMID: 29675466
DOI: 10.1126/sciadv.aao5416

[…] We classified all the proteins from five Papilio species (P. memnon, P. polytes, P. xuthus, P. machaon, and P. glaucus) into orthologous groups using Proteinortho (). This tool constructs groups on the basis of an all-against-all alignment of Blastp. The definition of an orthologous relationship between proteins was as follows: e value, ≤10 to 5; i […]

library_books

Whole genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow

2018
Sci Adv
PMCID: 5884691
PMID: 29632892
DOI: 10.1126/sciadv.aap9873

[…] l Feature Format (GFF) file.The annotated CDS for the bowhead whale was used to extract and translate the corresponding genomic regions from baleen whale genomes that were mapped to the bowhead whale Proteinortho version 5.11 screened protein sequences from all genomes listed in table S7. The baleen whale genomes were mapped to the bowhead whale genome and thus their CDSs have the same genomic coo […]

library_books

Genome Sequence, Assembly and Characterization of Two Metschnikowia fructicola Strains Used as Biocontrol Agents of Postharvest Diseases

2018
Front Microbiol
PMCID: 5891927
PMID: 29666611
DOI: 10.3389/fmicb.2018.00593

[…] O and Interproscan, using as blast database the fungal fraction of uniprot and swissprot databases ().The CAT webservice was used to find Pfam modules () in the proteins and assign them CAZy families.Proteinortho v. 5.16 was used to look for homologous proteins in the proteomes of M. fructicola 277, C. auris (BioProjects PRJNA342691 and PRJNA267757), M. bicuspidata (BioProject PRJNA207846) and C. […]

call_split

Routine Whole Genome Sequencing for Outbreak Investigations of Staphylococcus aureus in a National Reference Center

2018
Front Microbiol
PMCID: 5869177
PMID: 29616014
DOI: 10.3389/fmicb.2018.00511
call_split See protocol

[…] eny of the strains. The core-genes were selected from a pangenome constructed from 29 completely assembled S. aureus genomes (Supplementary Table ). Orthologs from the pangenome were identified using Proteinortho5 () using a cutoff of 70% of protein sequence similarity. Then the ortholog nucleic sequences were clustered with cd-hit (80% homology; ). For each cluster one or several representative s […]

library_books

Pangenomic Definition of Prokaryotic Species and the Phylogenetic Structure of Prochlorococcus spp.

2018
Front Microbiol
PMCID: 5857598
PMID: 29593678
DOI: 10.3389/fmicb.2018.00428

[…] Orthologous gene groups (OGGs) forming pangenomes were constructed using ProteinOrtho (Lechner et al., ) on annotated protein sequences. The sensitivity was controlled with BLAST (Altschul et al., ) E-value thresholds. Two E-value thresholds, 10−10 (Figures –) and 10−25 (S […]

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

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