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Roundup 2.0: Enabling Comparative Genomics for over 1800 Genomes

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3289913.pdf (70.53 KB)

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2012

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10.1093/bioinformatics/bts006

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Oxford University Press
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DeLuca, Todd F., Jike Cui, Jae-Yoon Jung, Kristian Che St. Gabriel, and Dennis Paul Paul Wall. 2012. Roundup 2.0: Enabling comparative genomics for over 1800 genomes. Bioinformatics 28(5): 715-716.

Abstract

Summary: Roundup is an online database of gene orthologs for over 1800 genomes, including 226 Eukaryota, 1447 Bacteria, 113 Archaea, and 21 Viruses. Orthologs are inferred using the Reciprocal Smallest Distance algorithm. Users may query Roundup for single-linkage clusters of orthologous genes based on any group of genomes. Annotated query results may be viewed in a variety of ways including as clusters of orthologs and as phylogenetic profiles. Genomic results may be downloaded in formats suitable for functional as well as phylogenetic analysis, including the recent OrthoXML standard. In addition, gene IDs can be retrieved using FASTA sequence search. All orthology results and source code are freely available.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3289913

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http://nrs.harvard.edu/urn-3:HUL.InstRepos:8519645

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