Department of Bioinformatics and Computational Biology

George Mason University

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GeneOrder and CoreGenes


Currently there are two tools, with different input ranges.

Note: pumpkins.ib3.gmu.edu will be going out of service, so please change your address page for the pumpkins-based sites.

GeneOrder

GeneOrder is designed for comparing two genomes, listing the order of the related, orthologs and putative orthologs, genes:

  1. GeneOrder2.0 gives an applet graph of the two genomes along with a table linking results to GenBank data.  The input size limit is approximately 350,000 bases- limiting comparisons to mitochondria, chloroplasts and viruses. http://binf.gmu.edu:8080/GeneOrder2.0
  2. GeneOrder3.0 extends the input limit to small bacterial genomes, ca. 500,000 bases to approx. 2.0Mb. http://binf.gmu.edu:8080/GeneOrder3.0

CoreGenes

  1. CoreGenes is designed to analyze two to five genomes simultaneously, generating a table of related genes- orthologs and putative orthologs.  These entries are linked to their GenBank data.  Further work will allow a researcher to characterize the relatedness of these genes:CoreGenes1.0 has an input limit of 350,000 bases. http://binf.gmu.edu:8080/CoreGenes1.0
  2. CoreGenes2.0 extends this limit to include small bacterial genomes, ca. 500,000 bases to approx. 2.0Mb. http://binf.gmu.edu:8080/CoreGenes2.0
  3. CoreGenes3.0beta. http://binf.gmu.edu:8080/CoreGenes3.0
  4. CoreGenes (CGUG) 3.1 adds a timer to on-line runs. Improves email delivery option (suggested for bacterial genomes which takes 20-40 min to run). Please limit email queuing to 5x small genomes or 2x bacterial genomes or else the software may crash. http://binf.gmu.edu:8080/CoreGenes3.1/

 

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Last Updated July 30, 2009