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cnci website  

It is a challenge to classify protein-coding or non-coding transcripts, especially those re-constructed from high-throughput sequencing data of poorly annotated species. We developed and evaluated a powerful signature tool, Coding-Non-Coding Index (CNCI), by profiling adjoining nucleotide triplets to effectively distinguish protein-coding and non-coding sequences independent of known annotations. CNCI is effective for classifying incomplete transcripts and sense-antisense pairs. The implementation of CNCI offered highly accurate classification of transcripts assembled from whole-transcriptome sequencing data in a cross-species manner, that demonstrated gene evolutionary divergence between vertebrates, and invertebrates, or between plants, and provided a long non-coding RNA catalog of orangutan.

Environment Modules

Run module spider cnci to find out what environment modules are available for this application.

System Variables

  • HPC_CNCI_DIR - installation directory
  • HPC_CNCI_BIN - executable directory


If you publish research that uses cnci you have to cite it as follows:

Liang Sun, Haitao Luo, Dechao Bu, Guoguang Zhao, Kuntao Yu, Changhai Zhang, Yuanning Liu, RunSheng Chen and Yi Zhao* Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. Nucleic Acids Research (2013), doi: 10.1093/nar/gkt646