FETx ------------------------------------------------------------------------------ FETx is a plugin for GFF-Ex. FETx translates coordinates of user specified feature into sequences using GFF-Ex. System Requirements ------------------------------------------------------------------------------ 1. OS Platform:- Linux 2. Perl 4.0, or above 3. GFF-Ex_v2.1 Required Input Files ----------------------------------------------------------------------------- 1. Gff/Gtf file (.gff/.gtf) 2. Corresponding Genome Sequence file in fasta format. (.fa, .fasta, .fna, etc.) 3. feature of interest specified within gff file. (gene, exon, etc) Inputs Example Files ----------------------------------------------------------------------------- 1. Gtf File: /FETx/examples/example.gtf 2. Genome: /FETx/examples/sequence.fasta Output Files Preffix(Plugin Name)_Suffix(Input multicolumnfile/sequencefile) ----------------------------------------------------------------------------- 2. Desired Sequences - OUTPUTFILE: fetx_(feature-name)_(input "genome" filename) Installation ----------------------------------------------------------------------------- 1. Download FETx.tar.gz 2. sudo -s 3. gunzip FETx.tar.gz 4. tar -vxf FETx.tar 5. cd FETx 6. ./install.sh ------configures the installtion path and install the program 7. source GFF_INSTALLATION_PATH/.gff_profile [NOTE:Please run this command prior to the execution of FETx] 8. Using same terminal move to the directory containing the input files and run COLx [GFF_INSTALLATION_PATH/gffex -pl fetx -in -db -ft ] Usage ----------------------------------------------------------------------------- 1. Using terminal, move to the working directory containing your input files. 2. run FETx using command "GFF_INSTALLATION_PATH/gffex -pl [fetx] -in [gff-file] -db [seqeuncefile] -ft featurename" GFF_INSTALLATION_PATH/gffex -pl fetx -in input -db seqeunce.fasta -ft gene ########################################################################################## ##################################### EXAMPLE RUN ######################################## ########################################################################################## INPUT1 (GFF/GTF) ------ XXXX XXXX gene 1 10 XXXX XXXX XXXX XXXX XXXX XXXX exon 11 15 XXXX XXXX XXXX XXXX XXXX XXXX gene 20 28 XXXX XXXX XXXX XXXX XXXX XXXX start_codon 35 44 XXXX XXXX XXXX XXXX INPUT2 ------ >example CGATGCTATGCTGTAGCGATGCGACATGCATGCATGCTAGCGATCGGCGACGTAGCGATCGTAGCAGCTACATCAC ACTATCGTAGCTAGTCGTGCAGCTGCTAGTCGATGCAGCGCTAGCTCGAGCTCTGTGCATGTAGCACGACTAGCCA TCTACGATGCTAGTCTAGCAGCGATCGTAGTCACTGACGATC [FETx_run]$ source GFF/INSTALLATON_PATH/gff_profile [FETx_run]$ GFF_INSTALLATION_PATH/gffex -pl fetx -in INPUT1 -db INPUT2 -ft gene OUTPUT ------ >Feature_Description CGATGCTATG >Feature_Desscription TGCGACATG ########################################################################################## ##################################### EXAMPLE RUN ######################################## ########################################################################################## DeveloperZ Information ------------------------------------------------------------------------------ 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 ------------------------------------------------------------------------------ 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.