BMix – Probabilistic Modeling of Occurring Substitutions in PAR-CLIP data

BMix

:: DESCRIPTION

BMix is a toolbox for analysing PAR-CLIP data and detecting T-to-C substitutions induced following RNA-protein cross-linking.

::DEVELOPER

the Computational Biology Group (CBG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BMix

:: MORE INFORMATION

Citation:

BMix: Probabilistic modeling of occurring substitutions in PAR-CLIP data.
Golumbeanu M, Mohammadi P, Beerenwinkel N.
Bioinformatics. 2015 Sep 5. pii: btv520.

PAR-CLIP HMM 0.1.0 – Bayesian hidden Markov models to identify RNA-protein interaction sites in PAR-CLIP

PAR-CLIP HMM 0.1.0

:: DESCRIPTION

PAR-CLIP HMM (rcpphmmparclip) provides an integrative model to establish a joint distribution of read and mutation counts. To pinpoint the interaction sites at single base-pair resolution, we adopts non-homogeneous hidden Markov models that incorporate the nucleotide sequence.

::DEVELOPER

The Quantitative Biomedical Research Center 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • R

:: DOWNLOAD

 PAR-CLIP HMM

:: MORE INFORMATION

Citation

Biometrics. 2014 Jun;70(2):430-40. doi: 10.1111/biom.12147. Epub 2014 Feb 24.
Bayesian hidden Markov models to identify RNA-protein interaction sites in PAR-CLIP.
Yun J1, Wang T, Xiao G.

BackCLIP 2.1 – Tool to Identify common RNA Background in PAR-CLIP Datasets

BackCLIP 2.1

:: DESCRIPTION

BackCLIP is a tool to identify the presence of common RNA background in a PAR-CLIP dataset.

::DEVELOPER

BackCLIP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 BackCLIP

:: MORE INFORMATION

Citation

BackCLIP: a tool to identify common background presence in PAR-CLIP datasets.
Reyes-Herrera PH, Speck-Hernandez CA, Sierra CA, Herrera S.
Bioinformatics. 2015 Jul 29. pii: btv442.

PARalyzer 2.0 – PAR-CLIP Data Analyzer

PARalyzer 2.0

:: DESCRIPTION

PARalyzer is a tool for mapping high-confidence sites from PAR-CLIP (photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation) deep-sequencing data.

::DEVELOPER

Uwe Ohler’s Research Group

:: REQUIREMENTS

  • Linux
  • Java
  • Bowtie

:: DOWNLOAD

 PARalyzer

:: MORE INFORMATION

Citation

Genome Biol. 2011 Aug 18;12(8):R79. doi: 10.1186/gb-2011-12-8-r79.
PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data.
Corcoran DL, Georgiev S, Mukherjee N, Gottwein E, Skalsky RL, Keene JD, Ohler U.

PARma 1.0 – PAR-CLIP data microRNA Assignment

PARma 1.0

:: DESCRIPTION

PAR-CLIP is a high-throughput method to identify binding sites of RNA binding proteins.

::DEVELOPER

Institute for Bioinformatics, Ludwig-Maximilians-Universität München

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Java

:: DOWNLOAD

 PAR-CLIP

:: MORE INFORMATION

Citation

PARma: identification of microRNA target sites in Argonaute PAR-CLIP data.
Erhard F, Dolken L, Jaskiewicz L, Zimmer R.
Genome Biol. 2013 Jul 29;14(7):R79.