CPC2 standalone

• 2019-11-23 15:30, Yang Ding
  • Now CPC2 supports both Python 2 and Python 3 (thanks for help from HyperOdin)

1 Pre-requisite:

a. Biopython package: a local version could be downloaded from http://biopython.org/wiki/Download

2 Install

a. Unpack the tarball:

tom@linux$ gzip -dc CPC2-beta.tar.gz | tar xf -

b. Build third-part packages:

tom@linux$ cd CPC2-beta
tom@linux$ export CPC_HOME="$PWD"
tom@linux$ cd libs/libsvm
tom@linux$ gzip -dc libsvm-3.18.tar.gz | tar xf -
tom@linux$ cd libsvm-3.18
tom@linux$ make clean && make

3 Run the predict

tom@linux$ cd $CPC_HOME
tom@linux$ bin/CPC2.py -i (input_seq) -o (result_in_table)

example: tom@linux$ bin/CPC2.py -i data/example.fa -o example_output

4 Output result

The result is in table format (plain text delimited by tab).

Default output:
#ID transcript_length peptide_length Fickett_score pI ORF_integrity coding_probability label

Set '--ORF' to output the start position of longest ORF:
#ID transcript_length peptide_length Fickett_score pI ORF_integrity ORF_Start coding_probability label

Contact

See the website for tutorial and more details. (http://cpc2.cbi.pku.edu.cn)

This is a beta version of CPC2, if have any questions please report to us.

Contact: cpc@mail.cbi.pku.edu.cn

About CPC2

Here are some example commands:

• To run a basic test: cpc2 -i data/example.fa -o test_output
• To check the reverse strand: cpc2 -i data/example.fa -o test_output -r
• To output the longest ORF: cpc2 -i data/example.fa -o test_output --ORF
• To get help: cpc2 --help

Coding Potential Calculator distinguishes protein-coding from non-coding RNAs based on the sequence features of the input transcripts. CPC2 is an updated version of CPC1, designed to be faster and more accurate in discriminating coding and non-coding transcripts.

Input Requirements

CPC2 accepts RNA transcript sequences in both FASTA format and GTF/GFF/BED format.

FASTA format:

• Size: Less than 100,000 lines in input box (online) and no line limitation in batch mode. Maximum upload file size is 50 Mb.
• Name: Sequence names must begin with ‘>’. Characters after a blank space in the ID will be discarded.
• Sequence: Only characters found in DNA and RNA sequences are allowed.

GTF/GFF/BED format:

• Supported formats: BED6, BED12, GTF, and GFF.
• Size: Less than 50,000 lines. Maximum upload file size is 50 Mb.
• Supported genomes for GTF/GFF/BED: Human (hg38, hg19), Chimpanzee (panTro4), Mouse (mm10), Rat (rn6), Zebrafish (danRer7), Xenopus (xendTro3), Fruitfly (dm6).
• Note: Inputting in BED format might slow down processing.

Features

• Speed and Accuracy: CPC2 employs a novel discriminative model based on sequence intrinsic features, making it significantly faster than CPC1 and other popular tools, while also offering superior accuracy.
• Species-Neutral: The model used in CPC2 is species-neutral, making it suitable for analyzing transcriptomes from a wide range of organisms, including non-model organisms.
• Output: Results include sequence ID, coding/noncoding classification, coding probability, scores for putative peptide length, Fickett TESTCODE score, putative isoelectric point, and ORF integrity.

For more detailed information on the web server, input/output formats, and additional features like BLAST integration, please refer to the original CPC2 documentation and publication.

Maintained for PyPI by:

Pranjal Pruthi Project Scientist, BioinformaticsOnLine organization Email: mail@pranjal.work

Original Publication:

Kang Y. J., Yang D. C., Kong L., Hou M., Meng Y. Q., Wei L., Gao G. 2017. CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features. Nucleic Acids Research 45(Web Server issue): W12–W16.