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CNCI specifications


Unique identifier OMICS_09888
Alternative name Coding-Non-Coding Index
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes


No version available



  • person_outline Yi Zhao

Publication for Coding-Non-Coding Index

CNCI citations


Genome wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs during Cryptosporidium baileyi infection

BMC Genomics
PMCID: 5946474
PMID: 29747577
DOI: 10.1186/s12864-018-4754-2

[…] Four analytic tools, namely coding-non-coding-index (CNCI) [], coding potential calculator (CPC) [], phylogenetic codon substitution frequency (PhyloCSF) [] and Pfam-scan [], were used to effectively distinguish protein-coding and non-coding sequences. […]


Comprehensive analysis of coding lncRNA gene co expression network uncovers conserved functional lncRNAs in zebrafish

BMC Genomics
PMCID: 5954278
PMID: 29764394
DOI: 10.1186/s12864-018-4458-7

[…] nd transcript length greater than 2000. Those foregone coding-genes or transcripts with size less than 200 nt were filtered out. Then, lncRNA candidates were identified by CPC (Version 0.9-r2) [] and CNCI (Version 2) []. At last, all zebrafish lncRNAs stemming from RNA-seq datasets and other publicly available sources were integrated together using the Cuffmerge program in the Cufflinks suite. […]


Genome wide differential expression profiling of mRNAs and lncRNAs associated with prolificacy in Hu sheep

Biosci Rep
PMCID: 5920141
PMID: 29439142
DOI: 10.1042/BSR20171350

[…] red using a minimum length and exon number threshold. Transcripts with lengths exceeding 200 nts, and with more than two exons, were selected as lncRNA candidates, and were further screened using cpc/cnci/pfam/cpa, which can distinguish protein-coding from non-coding genes. Then, the different types of lncRNAs, including lincRNA, intronic lncRNA, and antisense lncRNA, were selected using cuffcompa […]


Cross species inference of long non coding RNAs greatly expands the ruminant transcriptome

PMCID: 5926538
PMID: 29690875
DOI: 10.1186/s12711-018-0391-0

[…] applied similarly conservative classification criteria. For cattle, 9778 lncRNAs were obtained [], each of which were longer than 200 bp, considered non-coding by the classification tools CPC [] and CNCI [], lacked sequence similarity to the NCBI nr [] and Pfam databases [], and had a normalised read count higher than 25 in at least two of three replicates per tissue for 18 tissues. For human, 17 […]


Long noncoding RNAs are associated with metabolic and cellular processes in the jejunum mucosa of pre weaning calves in response to different diets

PMCID: 5940403
PMID: 29765519
DOI: 10.18632/oncotarget.24898

[…] oinformatic algorithms and pipelines have been developed []. In our study, four different, independent bioinformatic lncRNA prediction tools were applied in parallel: three alignment-free algorithms, CNCI [Coding-Non-Coding Index, [],], PLEK [(Predictor of long non-coding RNAs and messenger RNAs based on k-mer scheme, [], […]


Characterization of lncRNAs involved in cold acclimation of zebrafish ZF4 cells

PLoS One
PMCID: 5892903
PMID: 29634734
DOI: 10.1371/journal.pone.0195468

[…] NONCODE2016 database and filter out the same or similar transcripts []. The remaining unknown transcripts were filtered by length 200 nt, exon number 1, ORF 300 nt. CPC (Coding Potential Calculator), CNCI (Coding Non-Coding Index) and Pfam were used to delete transcripts with coding potential [–]. Finally, we calculated fragments per kilobase per million mapped reads (FPKM) of per transcript and r […]


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CNCI institution(s)
Bioinformatics Research Group, Advanced Computing Research Laboratory, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
CNCI funding source(s)
Training Program of the Major Research plan of the National Natural Science Foundation of China (91229120); International Science and Technology Cooperation Projects (2010DFA31840 and 2010DFB33720)

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