#CNCI About CNCI 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 nucl...
and are therefore time-consuming and restricted by prior annotations. Recently, a software tool named Coding-Non-Coding Index (CNCI) was developed [17]. It discriminates coding from non-coding transcripts using
As a class, the 74 aRs showed a much lower coding potential compared with mRNA in our dataset using each of three programs: Coding Potential Calculator (CPC2),44 Coding-Potential Assessment Tool (CPAT),45 and Coding-Non-Coding Index (CNCI)46 (p < 0.0001 in each case; Kruskal-Wallis test...
Subsequently, gene coding ability was predicted for the screened transcripts in the second step and the transcripts with coding potential were removed using coding potential calculator (CPC, version 0.9-r2)30, coding-non-coding index (CNCI, version 1.0)31, the protein families database (Pfam, ...
we removed all transcripts with coding potential using the Coding–Non-Coding Index (CNCI)46and the Coding Potential Calculator (CPC)47with default parameters. Finally, we eliminated all transcripts homologous to canonical ncRNAs stored in the following databases: miRBase19, tRNAdb20, snoRNAbase21,...
CNCI: Coding-Non-Coding Index TPM: Transcripts per million GAPDH: Glyceraldehyde-3-phosphate dehydrogenase References Zhou JX, Li GL, Xia H, Xiao B, Bi FF, Liu D, et al. Cerebral Schistosomiasis japonica without gastrointestinal system involvement. Surg Neurol. 2009;71:481–6. Article Pu...
On the other hand, alignment-free methods like the Coding Potential Assessment Tool (CPAT), Coding-Non-Coding Index (CNCI), PLEK (predictor of long non-coding RNAs and messenger RNAs based on an improved k-mer scheme), lncScore, Coding-Non-Coding Identifying Tool (CNIT), CPPred and Deep...
CNCI: Coding non-coding index CPC: Coding potential calculator Cq: Quantitation cycle FPKM: Fragments per kilobase of transcript per million mapped reads GO: Gene ontology KEGG: Kyoto Encyclopedia of Genes and Genomes lncRNA: Long non-coding RNA lincRNA: Long intergenic non-coding RNA...
Among the remaining transcripts, those with length longer than 200 bp were selected for the protein-coding-score test to calculating the Coding Potential Calculator (CPC)39 and Coding-Non-Coding Index (CNCI)40. The differentially expressed lncRNAs were selected that had |log2 (fold change) |>...
Coding ability was predicted using coding-non-coding-index (CNCI), coding potential calculator (CPC) and coding-potential assessment tool (CPAT). The expression analysis was performed using Cuffdiff. Expressed profile of lncRNAs and mRNAs in brains of mice upon RABV infection were shown in Tables...