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Publication for Proteinortho
Comparative Genomics and Mutational Analysis Reveals a Novel XoxF Utilizing Methylotroph in the Roseobacter Group Isolated From the Marine Environment
[…] 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 […]
Parallel evolution of Batesian mimicry supergene in two Papilio butterflies, P. polytes and P. memnon
[…] 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 […]
Whole genome sequencing of the blue whale and other rorquals finds signatures for introgressive gene flow
[…] 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 […]
Genome Sequence, Assembly and Characterization of Two Metschnikowia fructicola Strains Used as Biocontrol Agents of Postharvest Diseases
[…] 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. […]
Routine Whole Genome Sequencing for Outbreak Investigations of Staphylococcus aureus in a National Reference Center
[…] 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 […]
Pangenomic Definition of Prokaryotic Species and the Phylogenetic Structure of Prochlorococcus spp.
[…] 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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