Download

Here is RGCap download links

1. Executable.
2. Scripts
3. Models

General instruction for RGPred

RGPred is a SVM based high-throughput plant resistance gene prediction pipeline from plant genome, transcriptome and proteome sequences. It have been developed for the prediction of four class of resistance gene through the combination of binary classifier i.e. CNL, TNL, RLK and RLP. Sequence composition (amino-acid, dipeptide, tripeptide,multiplet,charge,hydrophobicity) propeties of resistance genes have been used for the classification of plant resistance gene from non plant resistance genes. RGPred uses Augustus for resistance gene prediction for genome sequences and Transdecoder for transcriptome sequence

Requirement

1. Unix based opertating OS
2. Perl version >5.0
3. Augustus version >=3.3
4. Transdecoder version >=5.2

Installation

1.Augustus forgGenome sequences: I. Download Augustus (http://bioinf.uni-greifswald.de/augustus/binaries/augustus-3.3.2.tar.gz) and install as per augustus installation instruction in augustus README file II. Set environment variable AUGUSTUS_CONFIG_PATH: export AUGUSTUS_CONFIG_PATH=/my_path_to_AUGUSTUS/augustus/config/ OR Run through augustus command line option: --AUGUSTUS_CONFIG_PATH=/my_path_to_AUGUSTUS/augustus/config/ III. Run augustus --species=arabidopsis --gff3=on --uniqueGeneId=true --codingseq=on genomic_seq.fasta

2.Transdecoder for transcriptome sequences: I. Download Transdecoder (https://github.com/TransDecoder/TransDecoder/archive/TransDecoder-v5.2.0.tar.gz) and install ase per transdecoder instruction II. Export Transdecoder path: export PATH=$PATH:~/path to/TransDecoder-TransDecoder-v5.2.0/ III. Check the Transdecoder commands from terminal: TransDecoder.LongOrfs/TransDecoder.Predict

Running RGPred

For convenience, put input file in RGPred folder and run

perl RGPred.pl --Infile=FVXD.fna --Seqtype=T --Score_cutof=0.1 --Tempfile=YES

for more detail information of running parameters, run help

perl RGPred.pl --help