Journal
NUCLEIC ACIDS RESEARCH
Volume 41, Issue 17, Pages -Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkt646
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Funding
- Training Program of the Major Research plan of the National Natural Science Foundation of China [91229120]
- International Science and Technology Cooperation Projects [2010DFA31840, 2010DFB33720]
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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. This study 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. CNCI software is available at http://www.bioinfo.org/software/cnci.
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