Copyright (c) 2001. George Mason University. All rights reserved.

CoreGenes HELP Manual
 
NOTE: CoreGenes now only reports common genes across
all requested genomes, ie the gene has to have BLAST
similarities in all genomes in order to appear on
the table. Another version and algortihm for
CoreGenes is being developed that will be comprehensive.
 
 
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). Presented in Durham, NC Mar 02. H.
J. Caulfield, et. al., eds. 1186-1192.
ALSO selected for reprinting @ Information Sciences
146 (1-4): 127-135.
 
 
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.
 
 
Mazumder, R., Kolaskar, A. and Seto, D. (2001).
GeneOrder: Comparing the order of genes in small
genomes. Bioinformatics 17: 162-166.
 

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 a
"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:
It is not necessary to have five genomes; you may use two to five total!!!!

For example, you can enter X73487 (human adenovirus HAD12 genome)
into the "genome 1" box and U40839 (ovine adenovirus OAV287) into
the "genome 2" box, etc.

You can compare small genomes such as viruses, mitochondria and
chloroplasts. CURRENTLY, Please do not use genomes larger than 250 kb.
Any genomes over 30 kb will take more than 5 minutes.
 

ALIGNMENT
You may choose to use the default BLASTP threshold value of 75 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 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 orthologs in common BETWEEN the genomes.

AGAIN, this 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
CoreGenes has been tested on Sun (Netscape), SGI (Netscape),
Macintosh (Microsoft Internet Explorer and Netscape 4.78), 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.

{This is dependent on "Java" running on your computer, especially with
Macintoshes.
We are using either unix platforms or PC with Internet Explorer. This
is dependent on "Java" running on your computer, especially with
Macintoshes.

PLEASE make sure the MAC has the "Java Accelerator for PowerPC" in the
CORRECT folder.}

PRINTING
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!!!