
  +---------------------------------------------------------------------+
  | CPPred:coding potential prediction                                  |
  |                                                                     |
  |                 http://rnabinding.com/CPPred                        | 
  +---------------------------------------------------------------------+


1) Introduction

CPPred is a coding potential prediction tool, which is based on SVM to distinguish
ncRNAs from coding RNAs using sequence features, such as ORF length, ORF coverage, 
ORF integrity, Fickett score, Hexamer score, PI, Gravy, Instability index and 
CTD-encoded features.

2) Uncompress and usage of CPPred

tar -zxvf CPPred.tar.gz

cd CPPred/bin

python CPPred.py -i input_RNA.fa -hex Hexamer.tsv -r range -m model -spe species -o result

(Here, "input_RNA.fa" is RNAs file in FASTA format. "Hexamer.tsv" is a pre-built hexamer 
frequency table. "range" is pre-built training range file. "model" is pre-built training model. 
"species" is the model of the species to choose (Human,Integrated). The "result" file in it 
is the final result for each prediction.)

3) Example
python CPPred.py -i ../data/Human_coding_RNA_test.fa  -hex ../Hexamer/Human_Hexamer.tsv -r ../Human_Model/Human.range -mol ../Human_Model/Human.model -spe Human -o Human_coding.result 
python CPPred.py -i ../data/Human_ncrna_test.fa -hex ../Hexamer/Human_Hexamer.tsv -r ../Human_Model/Human.range -mol ../Human_Model/Human.model -spe Human -o Human_ncrna.result 

python CPPred.py -i ../data/Mouse_coding_RNA_test.fa  -hex ../Hexamer/Human_Hexamer.tsv -r ../Human_Model/Human.range -mol ../Human_Model/Human.model -spe Human -o Mouse_coding.result 

python CPPred.py -i ../data/Zebrasfish_coding_RNA_test.fa  -hex ../Hexamer/Human_Hexamer.tsv -r ../Human_Model/Human.range -mol ../Human_Model/Human.model -spe Human -o Zebrafish_coding.result 

python CPPred.py -i ../data/S.cerevisiae_coding_RNA_test.fa  -hex ../Hexamer/Human_Hexamer.tsv -r ../Human_Model/Human.range -mol ../Human_Model/Human.model -spe Human -o S.cerevisiae_coding.result 

python CPPred.py -i ../data/Fruit_fly_coding_RNA_test.fa  -hex ../Hexamer/Human_Hexamer.tsv -r ../Human_Model/Human.range -mol ../Human_Model/Human.model -spe Human -o Fruit_fly_coding.result 

python CPPred.py -i ../data/Integrated_coding_RNA_test.fa  -hex ../Hexamer/Integrated_Hexamer.tsv -r ../Integrated_Model/Integrated.range -mol ../Integrated_Model/Integrated.model -spe Integrated -o Integrated_coding.result 
python CPPred.py -i ../data/Integrated_ncRNA_test.fa  -hex ../Hexamer/Integrated_Hexamer.tsv -r ../Integrated_Model/Integrated.range -mol ../Integrated_Model/Integrated.model -spe Integrated -o Integrated_coding.result 


Contact: liushiyong@gmail.com 

Date: 2018-05-17
