Proteinortho protocols

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Proteinortho specifications

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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

 (27)
2018
PMCID: 5891927
PMID: 29666611
DOI: 10.3389/fmicb.2018.00593

[…] clustering was predicted using antismash website ()., the proteins involved in pulcherrimin biosynthesis in b. subtilis (yvnb, yvna, yvmc, yvmb, yvma, cypx; ) were downloaded from ncbi and used in a proteinortho v. 5.15 analysis with the maker predicted proteins of m. fructicola, with default parameters. the b. subtilis genes of interest were also blasted with blastp (blastall v. 2.2.26) […]

2018
PMCID: 5845213
PMID: 29523080
DOI: 10.1186/s12864-018-4576-2

[…] the antismash [] and smurf [] programs were used to predict sm clusters in a. arachidicola. phylogenomic analysis was performed by detecting orthologous proteins within other fungi using proteinortho (version 5.13) [], aligning them using muscle (version 3.8.31) [], and concatenating them into a 2 mb amino acid alignment using gblocks (version 0.91) []. we inferred our phylogenetic […]

2018
PMCID: 5764930
PMID: 29326206
DOI: 10.1128/genomeA.01369-17

[…] to 197 contigs of >1 kb, and accounting for total genome sizes ranging from 4,578,015 to 5,285,335 bp (). coding sequences (cdss) and orthologous genes were determined using prokka (v1.12) () and proteinortho (v5.15) (). between 4,204 and 5,035 coding dna sequences were identified in the corresponding genomes (). to predict and identify plasmids, serotypes, and acquired antibiotic resistance […]

2018
PMCID: 5953540
PMID: 29761785
DOI: 10.7554/eLife.33953.044

[…] data is available from the sra with project identifier srp018311., for the purposes of comparative genomics, gene conservation was calculated by first clustering into orthologous clusters with proteinortho5 () with a minimum 60% amino acid identity and 80% coverage. a presence/absence matrix de-replicated for co-occurring features was then used as the input for a random forest classifier […]

2018
PMCID: 5817090
PMID: 29491858
DOI: 10.3389/fmicb.2018.00214

[…] kb were discarded. between 43 and 197 contigs were obtained for the individual genomes, accounting for total genome sizes ranging from 4,578,015 to 5,285,335 bp ()., the tools prokka (v1.12) () and proteinortho (v5.15) () were used in order to determine coding sequences (cds), annotate the genomes and to detect orthologous genes. the two freely available perl scripts ‘cds_extractor’ (v0.7.1) […]


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Proteinortho in publications

 (188)
PMCID: 5934484
PMID: 29755426
DOI: 10.3389/fmicb.2018.00766

[…] 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 […]

PMCID: 5906075
PMID: 29675466
DOI: 10.1126/sciadv.aao5416

[…] lengths of coding sequences (cdss) were 1508 base pairs (bp) (table s3). these values were similar to those of p. polytes. the number of ortholog groups among the five papilio species estimated by proteinortho (identity, >25%; coverage, >50%) is shown in . the phylogenetic relationships of these species based on whole orthologous genes () were consistent with previous results (, ). […]

PMCID: 5884691
PMID: 29632892
DOI: 10.1126/sciadv.aap9873

[…] 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 […]

PMCID: 5891927
PMID: 29666611
DOI: 10.3389/fmicb.2018.00593

[…] () and of other biocontrol yeast strains (). the genes responsible for the biosynthesis of this siderophore were successfully identified only in b. subtilis (), and an analysis of orthology with proteinortho and blast showed no homology between the b. subtilis pulcherrimin gene cluster and the proteins predicted in m. fructicola. it is probable that the b. subtilis and m. fructicola genes […]

PMCID: 5869177
PMID: 29616014
DOI: 10.3389/fmicb.2018.00511

[…] 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 […]


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

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