Tag: Protein-RNA interaction

catRAPID – Prediction of Protein-RNA Interactions

catRAPID

:: DESCRIPTION

catRAPID is an algorithm to estimate the binding propensity of protein-RNA pairs. By combining secondary structure, hydrogen bonding and van der Waals contributions, catRAPID predicts protein-RNA associations with great accuracy.

::DEVELOPER

Tartaglia Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

catRAPID omics: a web server for large-scale prediction of protein-RNA interactions.
Agostini F, Zanzoni A, Klus P, Marchese D, Cirillo D, Tartaglia GG.
Bioinformatics. 2013 Nov 15;29(22):2928-30. doi: 10.1093/bioinformatics/btt495.

Piranha 1.2.1 – Peak-caller for CLIP- and RIP-Seq high-throughput Protein-RNA interaction data

Piranha 1.2.1

:: DESCRIPTION

Piranha is a peak-caller for CLIP- and RIP-Seq high-throughput protein-RNA interaction data. It accepts input in BED or BAM format and identifies regions of significant enrichment for reads. Piranha can also optionally incorporate additional external covariates into the peak-calling process, and identify sites of differential binding occupancy between cell types, conditions or development stages.

::DEVELOPER

The Smith Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC

:: DOWNLOAD

 Piranha

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Dec 1;28(23):3013-20. doi: 10.1093/bioinformatics/bts569. Epub 2012 Sep 28.
Site identification in high-throughput RNA-protein interaction data.
Uren PJ, Bahrami-Samani E, Burns SC, Qiao M, Karginov FV, Hodges E, Hannon GJ, Sanford JR, Penalva LO, Smith AD.