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#Roundup


Overview

Roundup is a large-scale orthology database. The orthologs are computed using the Reciprocal Smallest Distance (RSD) algorithm. This algorithm detects more (and more accurate) orthologs than reciprocal best blast hits and gives each ortholog a score based on its maximum likelihood evolutionary distance. Every release of Roundup downloads the latest genomes from UniProt and computes orthologs for them.

Papers

  • Roundup 2.0: Enabling comparative genomics for over 1800 genomes. Deluca TF, Cui J, Jung JY, St Gabriel KC, Wall DP. Bioinformatics. 2012
  • Phylogenetically informed logic relationships improve detection of biological network organization. Cui J, Deluca TF, Jung JY, Wall DP. BMC Bioinformatics. 2011
  • Detecting biological network organization and functional gene orthologs. Cui J, DeLuca TF, Jung JY, Wall DP. Bioinformatics. 2011
  • Cost-effective cloud computing: a case study using the comparative genomics tool, roundup. Kudtarkar P, Deluca TF, Fusaro VA, Tonellato PJ, Wall DP. Evol Bioinform Online. 2010
  • Ortholog detection using the reciprocal smallest distance algorithm. Wall DP, Deluca T. Methods Mol Biol. 2007
  • Roundup: a multi-genome repository of orthologs and evolutionary distances. Deluca TF, Wu IH, Pu J, Monaghan T, Peshkin L, Singh S, Wall DP. Bioinformatics. 2006
  • Detecting putative orthologs. Wall DP, Fraser HB, Hirsh AE. Bioinformatics. 2003

Visit: http://roundup.hms.harvard.edu