title: LncRNA-ID: Long non-coding RNA IDentification using balanced random forests.
abstract: BACKGROUND
  Long non-coding RNAs (lncRNAs), which are non-coding RNAs of length above 200 nucleotides, play important biological functions such as gene expression regulation. To fully reveal the functions of lncRNAs, a fundamental step is to annotate them in various species. However, as lncRNAs tend to encode one or multiple open reading frames, it is not trivial to distinguish these long non-coding transcripts from protein-coding genes in transcriptomic data.
  
  
  RESULTS
  In this work, we design a new tool that calculates the coding potential of a transcript using a machine learning model (random forest) based on multiple features including sequence characteristics of putative open reading frames, translation scores based on ribosomal coverage, and conservation against characterized protein families. The experimental results show that our tool competes favorably with existing coding potential computation tools in lncRNA identification.
  
  
  METHODS
  The scripts and data can be downloaded at https://github.com/zhangy72/LncRNA-ID.
authors: Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA.
authors: Rujira
authors: R
authors: Achawanantakun
authors: Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA.
authors: Jiao
authors: J
authors: Chen
authors: Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA.
authors: Yanni
authors: Y
authors: Sun
authors: Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA.
authors: Yuan
authors: Y
authors: Zhang
mesh_terms: D000818:Animals; D006801:Humans; D000069550:Machine Learning; D051379:Mice; D016366:Open Reading Frames; D011506:Proteins / Q000235:genetics; D062085:RNA, Long Noncoding / Q000235:genetics*; D012270:Ribosomes / Q000378:metabolism; D012984:Software
chemical_list: D011506:Proteins; D062085:RNA, Long Noncoding