This product includes software developed by the Apache Software Foundation
(http://www.apache.org/), as well as Ptolomy II (University of Calif. Regents).

Copyright (c) 2003. George Mason University. All rights reserved.

GeneOrder3.0 Help
 
 

REFERENCE:
Zafar, N., Mazumder, R. and Seto, D. (2002). Application of global
computational tools GeneOrder and CoreGenes to comparative analyses of
chordopoxvirus genomes. Proceedings of the Sixth Joint Conference on
Information Sciences (Fourth Conference on Computational Biology and
Genome Informatics). H. J. Caulfield, et. al., eds. 1186-1192.
ALSO in press @ Information Sciences 146 (1-4): 127-135.
 
Zafar, N., Mazumder, R. and Seto, D. (2001). Comparisons of gene
co-linearity in genomes using GeneOrder2.0. Trends in Biochemical
Sciences 26: 514-516.
 
Mazumder, R., Kolaskar, A. and Seto, D. (2001). GeneOrder: Comparing
the order of genes in small genomes. Bioinformatics 17: 162-166.

INPUT
NCBI Accession number input

Please make sure that you enter the NCBI-GenBank accession
number of full genomes into the Reference and Query boxes.
For example, you can enter NC_001460 and NC_002501 (human adenovirus HAD12 genome and Frog Ad)
the Query box.
 
 
NOTE, due to separate databases and GenBank definitions, currently only "NC_xxxxxx" numbers can be retreived.
These are what NCBI considers "curated."
 
 

You can compare small genomes such as viruses, mitochondria and
chloroplasts. Please do not use genomes larger than NC_004432 M.penetrans (1,358,633 bases, NC_004432)
currently.
 
The run time on a MacG4 is approx. 20 minutes.
 
  GeneOrder requires JAVA.
 

With the user proprietary database entry option, you may also
compare partial genomes from large organisms, subject to above limitations
currently.
 
OUTPUT: Table and dot-blot Graph. The graph is an applet (JAVA based)
which is not printable currently. You need to make a screenshot.
We are working on an alternative. Each dot is a whole gene from the
BLAST results

ALIGNMENT
You may choose to use the default BLASTP threshold values or use
more stringent threshold values. Each gene from the Query sequence
is compared against all of the genes from the Reference Genome
Database using BLASTP. Gene pairs which match with a BLASTP high
score above the threshold values that you enter in the boxes are
reported. You can specify up to three ranges, and your results will
be color coded based on the BLASTP scores you enter below.

OUTPUT
Initially there is a graphical output. The X and the Y axis denote
the gene numbers of the reference and query organisms. From the
graphical output the user can click on the hyperlink to view the
result in a tabular format. Hyperlinks from the table let the user
access individual protein information from the NCBI database.

TEST
The GeneOrder3.0 has been tested on IRIX SGI, Macintosh (Microsoft Internet
Explorer), and PC.

BUGS/SUGGESTION
Mac-Netscape Communicator 4.75 not compatible with GeneOrder3.0. The
software runs great on Mac-Internet Explorer. Could be a memory
allocation problem. Try to download the latest version of Netscape
and then run GeneOrder3.0.

DISCLAIMER
We provide you with this information and software "AS IS" and we
cannot take any responsibility if the program does not run as
desired. In no event shall the authors and/or George Mason
University or contributors to the software will be liable for any
direct, indirect, incidental, special, exemplary, or consequential
damages however caused.