Global Score

Global Score

To study long transcripts (>1000 nt), we use the fragmentation procedure, which is based on division of protein and RNA sequences into sub-regions. The signal coming from the binding propensities of individual fragments is integrated into a variable called Global Score that predicts the overall interaction ability of a protein-RNA pair. The introduction of Global Score allows the calculation of interactions with long non-coding RNAs, thus extending the general applicability of catRAPID (Bellucci et al. Nat Methods 2011).

The specific running time of our algorithm depends on the jobs queuing on our server, which has been optimized to run Signal Localization. To run the software locally, you should agree to the terms of the Academic License Agreement, which can be found here.

 

Submission reference: 199876

Submission label (optional)

Protein sequence (FASTA format - min 50 aa)

RNA sequence (FASTA format - min 1000 nt)

This module accepts text in fasta format. There is another version available that allows submission via file upload.

Fragmentation option (see Tutorial and Running times)

Uniform
Weighted

Score option (see Tutorial)

Global Score (raw profiles)
Signal Localization (normalized profiles using a reference set)

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Sample data

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Ptbp1 and Xist - example of an interacting protein-RNA pair [Signal localization option]

Rab7b and Myc - example of a non-interacting protein-RNA pair [Global Score option] (Siprashvili et al. 2012)