GeneOrder 4.0


COMPARE GENE ORDER BETWEEN TWO BACTERIAL GENOMES
  • Please do not use genomes greater than ~8Mb.
  • The result will be displayed in 1-30 minutes.
  • You may use the batch mode by entering your email address; (you may close the window after clicking submit and the results will be emailed to you).
  • The amount of time required for running is dependent on the genome size and server availability. It will take more time if more than one user is logged on.
  • Examples of bacterial genomes to try: Haemophilus ducreyi(NC_002940) and Haemophilus influenzae(NC_000907).

Enter input data below:
   Reference Sequence   
   Query Sequence   
   Database
   Email Address   
   Enter threshold BLAT high score ranges in the boxes below. Each gene from the Query sequence is compared to all of the genes from the Reference database using BLAT. Gene pairs which match with a BLAT high score above the threshold values that you enter below are reported. You can specify up to three ranges and your results will be color coded based on the BLAT scores you enter below.   
   Highest:       High:       Low:     
        

This version of GeneOrder4.0 has been developed by Padmanabhan Mahadevan and Donald Seto.
GeneOrder3.0 has been developed by Sashidhara Kundeti, Srikanth Celamkoti, Anjan Purkayastha and Donald Seto.
GeneOrder2.0 was intially developed by Raja Mazumder, Asok Kolaskar and Donald Seto.

This software is licensed from GMU and must not be modified without prior permission.
Copyright ©2004 George Mason University

References:

1. Mahadevan P. and Seto D. 2010. Rapid pair-wise synteny analysis of large bacterial genomes using web-based GeneOrder4.0.
BMC Research Notes 3:41.
2. Celamkoti S, Kundeti S, Purkayastha A, Mazumder R, Buck C and Seto D. 2004. GeneOrder3.0: software for comparing the order of genes in pairs of small bacterial genomes.
BMC Bioinformatics 5:52.
3. Nikhat Z, Mazumder R and Seto D. 2001. Comparisons of gene co-linearity in genomes using GeneOrder2.0.
Trends in Biochemical Sciences.26: 514-516.
4. Mazumder R, Kolaskar A and Seto D. 2001. GeneOrder compares the order of genes in small genomes.
Bioinformatics. 17:162-166.