CPC - Coding Potential Calculator

Pre-requisite

NCBI BLAST package: a local version could be downloaded from http://www.ncbi.nlm.nih.gov/blast/
A relatively comprehensive protein database. UniRef90 and NCBI nr should be both okay. The database should be named as "prot_db", and put under the data/ sub-directory.

Getting CPC source-code.

Now surppose your username is tom and your hostname is jerry, and so the prompt might be tom@jerry$ . Using the following command to get CPC standalone package.

tom@jerry$ wget http://cpc.cbi.pku.edu.cn/download/cpc-0.9.tar.gz

Then use this command to unpackage the compressed source-code package.

tom@jerry$ gzip -dc cpc-0.9.tar.gz | tar xf -

or just

tom@jerry$ tar -zxf cpc-0.9.tar.gz

Then complie and install the CPC package.


                                tom@jerry$ cd cpc-0.9 

                                tom@jerry$ export CPC_HOME="$PWD" 

                                tom@jerry$ cd libs/libsvm 

                                tom@jerry$ gzip -dc libsvm-2.8.1.tar.gz | tar xf - 

                                tom@jerry$ cd libsvm-2.8.1 

                                tom@jerry$ make clean && make 

                                tom@jerry$ cd ../.. 

                                tom@jerry$ gzip -dc estate.tar.gz | tar xf - 

                                tom@jerry$ cd estate 

                                tom@jerry$ make clean && make

Format BLAST database named as "prot_db", and put under the $CPC_HOME/data/ directory.

Run CPC


                                tom@jerry$ cd $CPC_HOME 

                                tom@jerry$ bin/run_predict.sh (input_seq) (result_in_table) (working_dir) (result_evidence)