GeneOrder3.0

COMPARE GENE ORDER BETWEEN TWO SMALL BACTERIAL GENOMES

(Please do not use genomes greater than ~2Mb)

(The result will be displayed in 1-30 minutes.You may use the batch mode by entering your email address; this returns the results to you by email (you may close the window) The amount of time required for running is dependent on the genome size and servers' availability. It will take more time if more than one user is logged on. Thank you for your patience)

PLEASE use accession numbers in the format of "NC_001454"-NOT-"L19443" due to GenBank requirements!

 
   Reference Sequence   
   Query Sequence   
   Database   
   Email Address   
   Enter threshold BLASTP 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 BLASTP. Gene pairs which match with a BLASTP 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 BLASTP scores you enter below.   
   Highest:       High:       Low:     
        
There are two display formats: graphical and tabular.
Currently the graph is an applet and must be saved as a "SCREEN SHOT".
Toggle between the two on the output page.

Click here to compare sequences not archived at NCBI

 README

Examples of small bacterial genomes to try:

Haemophilus ducreyi(NC_002940)
Haemophilus influenzae(NC_000907)

GeneOrder2.0 was intially developed by Raja Mazumder,Asok Kolaskar and Donald Seto.
This current version GeneOrder3.0 has been developed by Sashidhara Kundeti, Srikanth Celamkoti,
Anjan Purkayastha and Donald Seto.
This software is licensed from GMU and must not be modified without prior permission.
Copyright ©2004 George Mason University


References:
1. Nikhat, Z., R. Mazumder and D. Seto. 2001. Comparisons of gene co-linearity in genomes using GeneOrder2.0.
Trends in Biochemical Sciences.26: 514-516.
2. Mazumder, R., A. Kolaskar, D. Seto.2001. GeneOrder compares the order of genes in small genomes.
Bioinformatics. 17:162-166.
3. Kundeti, et al in preparation. 2003.

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