cpm+fcm

An efficient encoder for biological sequences using Copy Models (CPMs) and Finite-Context models (FCMs)

Access

It is required to clone the repository and give permitions for running the binaries:

git clone https://github.com/cobilab/cpm-fcm.git
cd cpm-fcm/
chmod +x cpm+fcm-enc
chmod +x cpm+fcm-dec

Running

For running cpm+fcm encoder:

./cpm+fcm-enc cpm+fcm.conf protein-file

This will generate protein-file.enc.

For running cpm+fcm decoder:

./cpm+fcm-dec protein-file.enc

This will generate protein-file.enc.dec.

Parameters

To see the options of the encoder:

./cpm+fcm-enc

This will output:

Usage: cpm+fcm-enc [ -v (verbose) ]
                   [ -buf buf_size (in millions of symbols, def 50) ]
                   [ -o encoded_file ]
                   cfg_file inp_file

To see the options of the decoder:

./cpm+fcm-dec

This will output:

Usage: cpm+fcm-dec [ -v (verbose) ]
                   [ -# (5% marks) ]
                   [ -o decoded_file ]
                   inp_file

Citation

On using this software/method please cite:

• Article in revision

Issues

For any issue let us know at issues link.

License

GPL v3.

For more information: http://www.gnu.org/licenses/gpl-3.0.html.