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Roundup 2.0: enabling comparative genomics for over 1800 genomes
Todd F DeLuca1, Jike Cui, Jae-Yoon Jung
1The Center for Biomedical Informatics, Harvard Medical School and Department of Pathology, Beth Israel Deaconess Medical Center, Boston MA 02115, USA. todd_deluca@hms.harvard.edu
Bioinformatics (Oxford, England)
|January 17, 2012
Summary
Roundup is a freely available online database that identifies gene orthologs across 1800+ genomes. It aids in functional and phylogenetic analysis using the Reciprocal Smallest Distance algorithm.
Area of Science:
- Bioinformatics
- Genomics
- Comparative Genomics
Background:
- Roundup is an online database providing gene ortholog information.
- It encompasses over 1800 genomes from Eukaryota, Bacteria, Archaea, and Viruses.
- The database is accessible at http://roundup.hms.harvard.edu.
Purpose of the Study:
- To provide a comprehensive resource for identifying and analyzing gene orthologs.
- To facilitate comparative genomic studies across a wide range of organisms.
- To offer flexible data retrieval and analysis options for researchers.
Main Methods:
- Gene orthologs are inferred using the Reciprocal Smallest Distance (RSD) algorithm.
- Users can query for single-linkage clusters of orthologous genes based on selected genomes.
- Results can be viewed as ortholog clusters or phylogenetic profiles and downloaded in formats like OrthoXML.
Main Results:
- The database contains orthologs for over 1800 genomes.
- It supports queries across diverse taxonomic groups (Eukaryota, Bacteria, Archaea, Viruses).
- Gene IDs can also be retrieved via FASTA sequence search.
Conclusions:
- Roundup serves as a valuable, freely accessible tool for genomic research.
- The database supports both functional and phylogenetic analyses of orthologous genes.
- Its comprehensive scope and flexible output formats enhance its utility for the scientific community.
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