Read Me

GOBU -- Gene Ontology Browsing Utility

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1. Our homepage
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https://gobu.sourceforge.io/

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2. Documentation
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The index.html file in manual sub-folder

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3. Running
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Windows users could run GOBU by double clicking gobuCmd.bat. In gobuCmd.bat, there
is only one command for running GOBU using Java Virtual Machine. Mac or
UN*X users could use this command to run GOBU, or try gobuCmd.sh.

NOTE: The option -Xmx2400M is a specific option of JVM for running GOBU with 2.4GB
memory, which means you should run GOBU under 64bit environment. You may change it
for larger amount of memory, but do not exceed the amount of physical memory of your
computer.

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4. The user folder
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We are now tring to put reference GOBU trees for common species in the user folder.
Now it includes trees for arabidopsis, worm (C. elegans), fly (D. melanogaster),
zebrafish (D. rerio), bacteria (E. coli), and yeast (S. cerevisiae). All based on
annotation files (release 2024-06-17) downloaded from the GO Consortium website
plus updated GFF3 files downloaded from Ensembl.

To build a customized GOBU reference tree, you may try the Annot2Tree.pl script
under the scripts folder. In general, a GFF3 file and a GAF file should be enough
for creating a reference tree.