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
  3. GeneOrde4.0 extends the input limit to large and commonly interested bacterial genomes, ca. 4Mb+. http://binf.gmu.edu:8080/GeneOrder4.0/

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. This software is currently limited to genomes 2Mb and smaller. http://binf.gmu.edu:8080/CoreGenes3.1/
  5. CoreGenes (CGUG) 3.5 adds a batch process for semi-automated processing. This software is currently limited to genomes 2Mb and smaller. It requires your email address to return the results as it will take additional time to process. http://binf.gmu.edu:8080/CoreGenes3.5/BatchCoreGenes.html

Human Adenovirus Genome/Genes percent ID Comparison Tool