GFF-EX
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GFF-Ex (gffex) is a Genome Feature extraction package which extracts Gene, Exon, Intron, Upstream Region of Gene (Promoters), Intergenic and CDS/cDNA sequences by just tweeting in the Genome Feature File (gff,gtf) along with the corresponding genome/chromosome.


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/Gtf file (.gff/.gtf)
2. Corresponding Genome Sequence file in fasta format. (.fa, .fasta, .fna, etc.)


Inputs Example Files
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1. Gtf File:	/GFF_v2.3/examples/example.gtf
2. Genome:	/GFF_v2.3/examples/sequence.fasta
3. Gff File:	/GFF_v2.3/examples/example2.gff
4. Genome2:	/GFF_v2.3/examples/sequence2.fasta


Output Files													Preffix(Feature Name)_Suffix(Input gff/sequence)
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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_v2.3.tar.gz
2. gunzip GFF_v2.3.tar.gz
3. tar -vxf GFF_v2.3.tar
4. cd GFF_v2.3
5. ./install.sh	<GFF_INTALLATION_PATH>		-------  configures the installtion path and install the program
6. source GFF_INSTALLATION_PATH/gff_profile	[NOTE:Please run this command prior to the execution of GFF-Ex]
7. Using same terminal move to the directory containing the input files and run GFF-Ex [GFF_INSTALLATION_PATH/gffex -in <gff_file> -db <genome_file>]

Usage
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1. Using terminal, move to the working directory containing your input files (GFF/GTF and Fasta files).
2. run Gff-Ex. using command "GFF_INSTALLATION_PATH/gffex -in [gff-file] -db [sequencefile]"		GFF_INSTALLATION_PATH/gffex -in example.gtf -db sequence.fasta OR GFF_INSTALLATION_PATH/gffex -in example2.gff -db sequence2.fasta


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. Script mounted and tested on Red-Hat EL 5.1.