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Comparative analysis of protein-coding and long non-coding transcripts based on RNA sequence features.

Authors
  • Volkova, Oxana A1
  • Kondrakhin, Yury V2, 3
  • Kashapov, Timur A3
  • Sharipov, Ruslan N3, 4
  • 1 * Laboratory of Gene Engineering, The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Prosp. Acad. Lavrentyeva, 10, Novosibirsk 630090, Russia.
  • 2 † Laboratory of Bioinformatics, Institute of Computational Technologies, The Siberian Branch of the Russian Academy of Sciences, Ul. Acad. Rzhanova, 6, Novosibirsk 630090, Russia.
  • 3 ‡ BIOSOFT.RU, Ltd, Ul. Russkaya, 41/1 Novosibirsk 630058, Russia.
  • 4 § Novosibirsk State University, Ul. Pirogova, 2, Novosibirsk 630090, Russia.
Type
Published Article
Journal
Journal of bioinformatics and computational biology
Publication Date
Apr 01, 2018
Volume
16
Issue
2
Pages
1840013–1840013
Identifiers
DOI: 10.1142/S0219720018400139
PMID: 29739305
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

RNA plays an important role in the intracellular cell life and in the organism in general. Besides the well-established protein coding RNAs (messenger RNAs, mRNAs), long non-coding RNAs (lncRNAs) have gained the attention of recent researchers. Although lncRNAs have been classified as non-coding, some authors reported the presence of corresponding sequences in ribosome profiling data (Ribo-seq). Ribo-seq technology is a powerful experimental tool utilized to characterize RNA translation in cell with focus on initiation (harringtonine, lactimidomycin) and elongation (cycloheximide). By exploiting translation starts obtained from the Ribo-seq experiment, we developed a novel position weight matrix model for the prediction of translation starts. This model allowed us to achieve 96% accuracy of discrimination between human mRNAs and lncRNAs. When the same model was used for the prediction of putative ORFs in RNAs, we discovered that the majority of lncRNAs contained only small ORFs ([Formula: see text][Formula: see text]nt) in contrast to mRNAs.

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