RP-BP 2.0.0 – Ribosome Profiling with Bayesian Predictions

RP-BP 2.0.0

:: DESCRIPTION

Rp-Bp is a Bayesian approach to predict, at base-pair resolution, ribosome occupancy and translation.

::DEVELOPER

Dieterich lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Python

:: DOWNLOAD

Rp-Bp

:: MORE INFORMATION

Citation

Malone B, Atanassov I, Aeschimann F, Li X, Großhans H, Dieterich C.
Bayesian prediction of RNA translation from ribosome profiling.
Nucleic Acids Res. 2017 Apr 7;45(6):2960-2972. doi: 10.1093/nar/gkw1350. PMID: 28126919; PMCID: PMC5389577.

RiboVision 1.15 – Visualization and Analysis of Ribosomes

RiboVision 1.15

:: DESCRIPTION

RiboVision is a modern open-source ribosome-information viewer website.

::DEVELOPER

Center for Ribosomal Origins and Evolution, Georgia Institute of Technology

:: SCREENSHOTS

RiboVision

:: REQUIREMENTS

  • Linux
  • Web Server

:: DOWNLOAD

 RiboVision

:: MORE INFORMATION

Citation:

Faraday Discuss. 2014;169:195-207. doi: 10.1039/c3fd00126a. Epub 2014 May 28.
RiboVision suite for visualization and analysis of ribosomes.
Bernier CR1, Petrov AS, Waterbury CC, Jett J, Li F, Freil LE, Xiong X, Wang L, Migliozzi BL, Hershkovits E, Xue Y, Hsiao C, Bowman JC, Harvey SC, Grover MA, Wartell ZJ, Williams LD.

RFMapp 20121217 – Ribosome Flow Model Application

RFMapp 20121217

:: DESCRIPTION

The RFMapp is a graphical user interface application, enabling the prediction of fundamental features of the gene translation process, including translation rates, ribosomal densities, protein abundance levels, and the relation between all these variables.

::DEVELOPER

Tamir Tuller’s Group

:: SCREENSHOTS

RFMapp

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 RFMapp

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Jun 15;28(12):1663-4. doi: 10.1093/bioinformatics/bts185. Epub 2012 Apr 11.
RFMapp: ribosome flow model application.
Zur H1, Tuller T.

Ribomap v1.2 – Isoform-level Ribosome Occupancy Estimation Guided by Transcript Abudance

Ribomap v1.2

:: DESCRIPTION

Ribomap is a package that generates isoform-level ribosome profiles from ribosome profiling data.

::DEVELOPER

Kingsford Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs
  • Sailfish/Salmon

:: DOWNLOAD

Ribomap

:: MORE INFORMATION

Citation

Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap.
Wang H, McManus J, Kingsford C.
Bioinformatics. 2016 Jun 15;32(12):1880-2. doi: 10.1093/bioinformatics/btw085