This "on the fly" application runs on Tomcat Servlet/JSP Engine
developed by the Apache Software Foundation (http://www.apache.org/)
and also utilizes Ptolemy II
system developed by The Regents of the University of California.

CoreGenes HELP Manual

NOTE: CoreGenes only lists genes in common across all genomes requested.

REFERENCE
1. Kundeti,S., S.Celamkoti and D.Seto. (CoreGenes2.0): Whole
genome analysis tool for identifying "core" genes in a set of small
bacterial genomes.

2. Zafar, N., Mazumder, R. and Seto, D. (2002). CoreGenes: A
computational tool for identifying and cataloging "core" genes in a set
of small genomes. BMC Bioinformatics 3:12.

INPUT
NCBI-GenBank accession numbers are to be used.

First:
Input the reference genome accession number. NOTA BENE, any
inaccurate or non-GenBank number results in an
"ERROR" message "The accession number is either not present in NCBi
database or the file for this accession number does not have any genes"

Please make sure that you enter the exact NCBI-GenBank accession
number of full genomes into the Reference and Query boxes.

Second and etc: You can compare small genomes such as viruses,
mitochondria and
chloroplasts. Small baterial genomes (<1Mb) can be analysed.

VERY IMPORTANT!
This is a hierarchical analysis. Meaning, if QUERY genome 1 does
not have a gene ortholog match to the reference genome, that PARTICULAR
gene is NOT used in subsequent QUERY 2 (and 3 and 4) analyses. AND
if QUERY genome 2 does not have a particular gene ortholog to QUERY
genome 1, THEN QUERY genome 3 etc will not be queried with respect to
that gene. It WILL show as orthologs between the reference genome
and query genome 1 but will NOT be visible for QUERY genomes 3 and 4
if they contain the ortholog while query genome 2 does not.

NOTA BENE, you NEED to do all permutations of the genomes in order to
have the best and most correct ortholog line-up!!! This is
HIERARCHICAL!

ONLY matches across all queried genomes will be displayed!!!!!

INPUT
NCBI-GenBank accession numbers are to be used.
---or-- for proprietary custom data entry
use link:
"Click here to compare genomes that are not archived at NCBI"

BATCH
For batch processing please provide your email address.

OUTPUT
Initially there is a graphical output AND/OR tabular displayóDEPENDING
on your platform. For the graph, the bottom x-axis represents the
REFERENCE genome. Each x-axis above this represents each query genome.
Dots are BLAST-matchbox in common BETWEEN the genomes.

The graph is hierarchical, so IF the ortholog is in the Reference AND
query 2 and 3 BUT not in query 2, THEN you will not see it displayed.

Should the table AND/OR the graph NOT appear post analysis, please
click the link for the display, DEPENDING on your particular platform.

From the TABLE output the user can click on the hyperlink to view
the individual protein information from the NCBI database.

TEST
The CoreGenes has been tested on Sun (Netscape), SGI (Netscape),
Macintosh (Microsoft Internet Explorer and Netscape 6.0), and Windows
(Explorer 5.0 and higher and Netscape Navigator with or without Java2
Plugin).

BUGS/SUGGESTION
Since this aplication outputs part of the result as a Java Applet it may

have a compatibility problem depending on
your settings and the browser. We have tested with Internet Explorer ver

5.5 and higher and Netscape Navigator ver 4.76 and higher (with or
without
Java2 Plugin) on Unix and Windows Plateform respectively. Please make
sure
the browser support for Applet is enabled. Also, for Mac Plateform,
please
make sure the MAC has the "Java Accelerator for PowerPC" installed and
it
is in the CORRECT folder

There could also be a memory allocation problem. Try to download the
latest
version of Netscape (ie, 6.0 for Mac) and then run CoreGenes again.
Or else try Explorer.

PRINTING
Due to the applet, printing needs to be done manually via your
computer's screen capture!!!

An alternative is to use the "Print Screen" option of your computer.
Either Apple + shift + 3 and look for "Picture 1" on your hard drive
(Macintosh-based) OR (PCs) Click window to activate, Alt + Print
Screen, then paste onto a document.

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.

This software is copyrighted by GMU. Please do not modify without
permission.

PLEASE email suggestions and thoughts to dseto@gmu.edu.

MANY thanks for using it! Good Hunting!!!