Tag: lncRNA

TERIUS 1.0.1 – Prediction of lncRNA via High-throughput Sequencing data

TERIUS 1.0.1

:: DESCRIPTION

TERIUS is a program designed to differentiate between long non-coding RNAs and transcripts with coding potential or transcripts that are actually 3’UTR fragments of mRNAs. TERIUS distinguishes these transcripts using two-step filtration process from bona fide lncRNAs.

:: DEVELOPER

BIG Lab. (BIOINFORMATICS & GENOMICS)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

TERIUS

:: MORE INFORMATION

Citation:

Choi SW, Nam JW.
TERIUS: accurate prediction of lncRNA via high-throughput sequencing data representing RNA-binding protein association.
BMC Bioinformatics. 2018 Feb 19;19(Suppl 1):41. doi: 10.1186/s12859-018-2013-9. PMID: 29504902; PMCID: PMC5836835.

LncDisease 1.41 – Predicting lncRNA-disease Associations

LncDisease 1.41

:: DESCRIPTION

LncDisease is a novel computational method and tool to predict the associations between lncRNAs and diseases

::DEVELOPER

the Cui Lab

:: SCREENSHOTS

LncDisease

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 LncDisease

:: MORE INFORMATION

Citation

LncDisease: a sequence based bioinformatics tool for predicting lncRNA-disease associations.
Wang J, Ma R, Ma W, Chen J, Yang J, Xi Y, Cui Q.
Nucleic Acids Res. 2016 Feb 16. pii: gkw093

lncFunTK – Functional Characterization of lncRNA by integrative network analysis

lncFunTK

:: DESCRIPTION

lncFunTK is a toolkit that integrates ChIP-seq, CLIP-seq, and RNA-seq data to predict, prioritize, and annotate lncRNA functions.

::DEVELOPER

Dr. Sun Hao’s Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Perl

:: DOWNLOAD

lncFunTK

:: MORE INFORMATION

Citation

Zhou J, Huang Y, Ding Y, Yuan J, Wang H, Sun H.
lncFunTK: a toolkit for functional annotation of long noncoding RNAs.
Bioinformatics. 2018 Oct 1;34(19):3415-3416. doi: 10.1093/bioinformatics/bty339. PMID: 29718162.

spongeScan – Detecting microRNA Binding Elements in lncRNA Sequences

spongeScan

:: DESCRIPTION

spongeScan is a web tool designed to identify and visualize lncRNAs acting as putative miRNA sponges, by searching for multiple miRNA binding sites in lncRNAs.

::DEVELOPER

The Genomics of Gene Expression Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

spongeScan: A web for detecting microRNA binding elements in lncRNA sequences.
Furió-Tarí P, Tarazona S, Gabaldón T, Enright AJ, Conesa A.
Nucleic Acids Res. 2016 May 19. pii: gkw443.

LncADeep – ab initio lncRNA Identification and Functional Annotation tool

LncADeep

:: DESCRIPTION

LncADeep is an ab initio lncRNA identification and functional annotation tool based on deep learning.First, LncADeep identifies lncRNAs by integrating sequence intrinsic and homology features based on deep belief networks. Second, LncADeep predicts lncRNA-protein interactions using sequence and structure features based on deep neural networks. Third, since accurate lncRNA-protein interactions can help to infer the functions of lncRNAs.

::DEVELOPER

ZhuLab, Peking Uiniversity, Beijing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WebBrowser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Bioinformatics. 2018 Nov 15;34(22):3825-3834. doi: 10.1093/bioinformatics/bty428.
LncADeep: an ab initio lncRNA identification and functional annotation tool based on deep learning.
Yang C, Yang L, Zhou M, Xie H, Zhang C, Wang MD, Zhu H.