System Requirements
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1. OS Platform:- Linux
2. Perl 4.0, or above


Required Input Files
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1. Gff file (.gff)
2. Corresponding Genome Sequence file in fasta format. (.fa, .fasta, fna, etc.)


Inputs Example Files
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1. Gff File:	/GFF_v2.1/examples/example.gff
2. Genome:	/GFF_v2.1/examples/sequence.fasta


Output Files												Preffix(Feature Name)_Suffix(Input GFF/Genome)
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1. Gene Sequences									- OUTPUT:	gene_(input "genome" filename)
2. Exon Sequences									- OUTPUT:	exon_(input "genome" filename)
3. CDS/cDNA Sequences									- OUTPUT:	CDS_(input "genome" filename)
4. mRNA Sequences									- OUTPUT:	mRNA_(input "genome" filename)
5. Intron Sequences									- OUTPUT:	intron_(input "genome" filename)
6. Intergenic Sequences									- OUTPUT:	intergenic_(input "genome" filename)
7. Promoter / Gene Upstream Sequences							- OUTPUT:	upstream_(input "genome" filename)


Installation
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1. Download GFF_v2.1.tar.gz
2. sudo -s
3. gunzip GFF_v2.1.tar.gz
4. tar -vxf GFF_v2.1.tar
5. cd GFF_v2.1
6. ./install.sh						    				-------  configures the file system and install the program


Usage
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1. Using terminal, move to the working directory containing your input files.
2. run Gff-Ex. using command " gffex -in [gff-file] -db [sequencefile]"			gffex -in example.gff -db sequence.fasta


Unstallation
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1. Just type "uninstallgffex" on the terminal.						uninstallgffex


Acknowledgements
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1. Dr. Dinesh Gupta
2. Mr. Abhinav Kaushik


DeveloperZ Information
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Achal Rastogi
(Dr. Dinesh Gutpa Group)
Research Fellow
Bioinformatics Facility
Structural & Computational Biology Laboratory
International Center for Genetic Engineering And Biotechnology
Aruna Asaf Ali Marg, New Delhi 110067 India
Email: achal@icgeb.res.in


NOTES
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1. Being in the directory containing input files is a prerequisite for running GFF-Ex, to avoid output errors.
2. Take care of the inputs, wrong inputs may fetch you with wrong results.
3. Remember to be super-user($ su) while installing. unistalling or executing GFF-Ex_v2.1.
4. Scripts mounted and tested on Red-Hat EL 5.1.