    --------   Gecko   -------

GEne Cluster detection in proKaryotic genOmes
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Thomas Schmidt        (tschmidt@cebitec.uni-bielefeld.de)

International NRW Graduate School in Bioinformatics and Genome Research
Center of Biotechnology (CeBiTec)
Bielefeld University
Germany
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Gecko is a tool for a systematic and efficient detection of gene
clusters in multiple prokaryotic genomes. It is based on a formal
model for gene clusters and is accompanied by an efficient
algorithm locating them. Gecko also provides an interactive
visualization of detected clusters and therefore supports the
analysis of the genes functional role. The algorithm and their use
in Gecko are described in detail in:

"Quadratic Time Algorithms for Finding Common Intervals in Two and More Sequences",
Thomas Schmidt and Jens Stoye,
Proceedings of the 15th Annual Symposium on Combinatorial Pattern Matching, CPM 2004

and

"GECKO: a tool for efficient gene cluster detection in prokaryotic genomes",
Thomas Schmidt, Christian Rckert, Jrn Kalinowski and Jens Stoye,
submitted

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Requirements:
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An installed version of the Java Runtime Environment JRE 1.4 or
higher. You can obtain an up-to-date version at
http://java.sun.com/j2se/1.4.2/download.html

Additional data:
----------------

"GeckoPaper_data.zip": The GeneClusterSession-File
(GeckoPaper.gcs) containing the Gecko-Session, from which the
results in the Gecko-Paper are obtained.

"sample_data.zip":
Some sample data to explore the functionality
of the whole software package (including GhostFam).

"COG_data.zip": A source file for gene cluster detection. It can
be loaded into Gecko as input data file.

All these files are available from the manual page of Gecko on the
BiBiServ:
http://bibiserv.techfak.uni-bielefeld.de/gecko/manual.html

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Installation:

Unpacking the zip archive (using winzip or unzip).

Run Gecko:
Change to the directory where the "Gecko.jar" file is located
Type:

java -jar -mx384m Gecko.jar


!!!!!!!!!!!!!!!!!!!!!!!!!!! IMPORTANT !!!!!!!!!!!!!!!!!!!!!!!!!
The parameter -mx384m allows the Java Virtual Machine to allocate
a maximum of 384 MB main memory for the computation. This is the
minimum space required to process the sample data from
"sample_data.zip", and to browse in the results from the
GeckoPaper.gcs file. However, to recalculate the gene clusters
from this file or from COG_data file the program requires more
main memory. Therefore it is necessary to run the program with the
parameter -mx1700m, avoiding an "out of memory error".
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!


Have much fun using GECKO!

