Proteinortho

Proteinortho: Detection of co-orthologs in large-scale analysis. Proteinortho is a tool to detect orthologous genes within different species. For doing so, it compares similarities of given gene sequences and clusters them to find significant groups. The algorithm was designed to handle large-scale data and can be applied to hundreds of species at one. Details can be found in Lechner et al., BMC Bioinformatics. 2011 Apr 28;12:124. To enhance the prediction accuracy, the relative order of genes (synteny) can be used as additional feature for the discrimination of orthologs. The corresponding extension, namely PoFF (manuscript in preparation), is already build in Proteinortho.


References in zbMATH (referenced in 9 articles )

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  1. Schaller, David; Geiß, Manuela; Stadler, Peter F.; Hellmuth, Marc: Complete characterization of incorrect orthology assignments in best match graphs (2021)
  2. Geiß, Manuela; Chávez, Edgar; González Laffitte, Marcos; López Sánchez, Alitzel; Stadler, Bärbel M. R.; Valdivia, Dulce I.; Hellmuth, Marc; Hernández Rosales, Maribel; Stadler, Peter F.: Best match graphs (2019)
  3. Hellmuth, Marc; Huber, Katharina T.; Moulton, Vincent: Reconciling event-labeled gene trees with MUL-trees and species networks (2019)
  4. Hellmuth, Marc; Seemann, Carsten R.: Alternative characterizations of Fitch’s xenology relation (2019)
  5. Warnow, Tandy (ed.): Bioinformatics and phylogenetics. Seminal contributions of Bernard Moret (2019)
  6. Hellmuth, Marc; Wieseke, Nicolas: On tree representations of relations and graphs: symbolic ultrametrics and cograph edge decompositions (2018)
  7. Hellmuth, Marc; Stadler, Peter F.; Wieseke, Nicolas: The mathematics of xenology: di-cographs, symbolic ultrametrics, 2-structures and tree-representable systems of binary relations (2017)
  8. Hellmuth, Marc; Hernandez-Rosales, Maribel; Huber, Katharina T.; Moulton, Vincent; Stadler, Peter F.; Wieseke, Nicolas: Orthology relations, symbolic ultrametrics, and cographs (2013)
  9. Lechner, Marcus; Findeiß, Sven; Steiner, Lydia; Marz, Manja; Stadler, Peter F.; Prohaska, Sonja J.: Proteinortho: detection of (Co-)Orthologs in large-scale analysis (2011) ioport