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OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software.

Kriventseva EV, Tegenfeldt F, Petty TJ, Waterhouse RM, Simão FA, Pozdnyakov IA, Ioannidis P, Zdobnov EM - Nucleic Acids Res. (2014)

Bottom Line: With the ever-increasing availability of genomic data, inference of orthology has become instrumental for generating hypotheses about gene functions crucial to many studies.We re-designed the entirety of the OrthoDB website from the underlying technology to the user interface, enabling the user to specify species of interest and to select the relevant orthology level by the NCBI taxonomy.The text searches allow use of complex logic with various identifiers of genes, proteins, domains, ontologies or annotation keywords and phrases.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland evgenia.kriventseva@unige.ch.

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OrthoDB web user interface. The orthologous group centric results panel is on the left and the query-building panel is on the right.
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Figure 1: OrthoDB web user interface. The orthologous group centric results panel is on the left and the query-building panel is on the right.

Mentions: OrthoDB is one of the largest resources of orthologs in terms of number of genomes covered, and has promoted the concept of hierarchical orthology since its conception (12). In this release we re-implemented the OrthoDB website and the graphical user interface (GUI) (Figure 1). Similar to some other resources, OrthoDB provides tentative functional annotations of orthologous groups and mapping to functional categories. Notably, OrthoDB provides the most extensive collection of functional annotations of the underlying genes linked to their original sources. Gene annotation is a complicated process that is hardly feasible without automation, which in turn can introduce errors. Although in many cases OrthoDB makes such errors in the collated annotation data apparent, search results with particularly discordant annotations should be considered with caution. The evolutionary annotations of the orthologs and statistics of gene architectures remain the distinguishing features of OrthoDB.


OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software.

Kriventseva EV, Tegenfeldt F, Petty TJ, Waterhouse RM, Simão FA, Pozdnyakov IA, Ioannidis P, Zdobnov EM - Nucleic Acids Res. (2014)

OrthoDB web user interface. The orthologous group centric results panel is on the left and the query-building panel is on the right.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383991&req=5

Figure 1: OrthoDB web user interface. The orthologous group centric results panel is on the left and the query-building panel is on the right.
Mentions: OrthoDB is one of the largest resources of orthologs in terms of number of genomes covered, and has promoted the concept of hierarchical orthology since its conception (12). In this release we re-implemented the OrthoDB website and the graphical user interface (GUI) (Figure 1). Similar to some other resources, OrthoDB provides tentative functional annotations of orthologous groups and mapping to functional categories. Notably, OrthoDB provides the most extensive collection of functional annotations of the underlying genes linked to their original sources. Gene annotation is a complicated process that is hardly feasible without automation, which in turn can introduce errors. Although in many cases OrthoDB makes such errors in the collated annotation data apparent, search results with particularly discordant annotations should be considered with caution. The evolutionary annotations of the orthologs and statistics of gene architectures remain the distinguishing features of OrthoDB.

Bottom Line: With the ever-increasing availability of genomic data, inference of orthology has become instrumental for generating hypotheses about gene functions crucial to many studies.We re-designed the entirety of the OrthoDB website from the underlying technology to the user interface, enabling the user to specify species of interest and to select the relevant orthology level by the NCBI taxonomy.The text searches allow use of complex logic with various identifiers of genes, proteins, domains, ontologies or annotation keywords and phrases.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland evgenia.kriventseva@unige.ch.

Show MeSH