GeneOrder 4.0 - Beta Fix Release

COMPARE GENE ORDER BETWEEN TWO BACTERIAL GENOMES

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).

GeneOrder plots will only work in Web Browsers that support Java plugins. The current versions of Edge, Firefox, Chrome and Safari do not natively support Java plugins. Please consult your browser documentation to determine how to enable Java.

Enter input data below:
	Reference Sequence
	Query Sequence
	Database
	Email Address
	Enter threshold BLAST 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 "BLAST-like alignment tool" (BLAT). Gene pairs which match with a BLAST 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 BLAST scores you enter below.
	Highest: High: Low:

There are two display formats: graphical and tabular.

Toggle between the two on the output page.

E-mail for help.

This version of GeneOrder4.0 has been developed by Padmanabhan Mahadevan and Donald Seto, and modified by Burton Post. 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, 2017 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.