Tag: Elucidation

PULSE – Positive Unlabeled Learning for Splicing Elucidation

PULSE

:: DESCRIPTION

PULSE is a semi-supervised learning algorithm, positive unlabeled learning for splicing elucidation, which uses 48 features spanning various categories.

::DEVELOPER

Kim Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX

:: DOWNLOAD

 PULSE

:: MORE INFORMATION

Citation

Cell Rep. 2015 Jul 14;12(2):183-9. doi: 10.1016/j.celrep.2015.06.031. Epub 2015 Jul 2.
Semi-supervised Learning Predicts Approximately One Third of the Alternative Splicing Isoforms as Functional Proteins.
Hao Y, Colak R, Teyra J, Corbi-Verge C, Ignatchenko A, Hahne H, Wilhelm M, Kuster B, Braun P, Kaida D, Kislinger T, Kim PM

kmerHMM 20120625 – DNA Motif Elucidation

kmerHMM 20120625

:: DESCRIPTION

To discover DNA motifs on PBM data, a computational pipeline using Hidden Markov Model (HMM) has been proposed and named, kmerHMM. The method has been compared with the state-of-the-arts methods on well-studied datasets. The results demonstrated the effectiveness of the proposed approach. In addition, belief propagations have been applied to reveal its multimodal motif discovery ability validated by wet-lab experiments.

::DEVELOPER

The Zhang Lab, University of Toronto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Weindows/Linux/MacOsX
  • R package /MatLab

:: DOWNLOAD

 kmerHMM

 :: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Sep;41(16):e153. doi: 10.1093/nar/gkt574. Epub 2013 Jun 29.
DNA motif elucidation using belief propagation.
Wong KC1, Chan TM, Peng C, Li Y, Zhang Z.