Bamboo: Bayesian Model of Protein Primary Sequence for Secondary Structure Prediction

Welcome to the Bamboo website which provides software for the methods described in the paper:

Q. Li, D. B. Dahl, M. Vannucci, H. Joo, J. W. Tsai (2014), Bayesian Model of Protein Primary Sequence for Secondary Structure Prediction, PLOS ONE, 9(10), e109832. Paper

The software is available in two ways:

  1. Through the web app below, and
  2. As a stand-only R package.
The package is available here bamboo_0.9.14.tar.gz and it depends on the rscala package. Both can be easily installed by running the following command at the R prompt:


source("http://bamboo.byu.edu/users/dahl/bamboo.byu.edu/install.R")

We ask that you use the R package instead of our web app if you need to obtain secondary structure predictions for many proteins. Further, the R package can use training data different from those in the paper.

This work is supported by NIH NIGMS R01 GM104972.


Inputs:

Amino Acid Sequence (using 1 letter codes without spaces):


Example MSA file

Results show below after clicking "Compute".

Sampling from the posterior distribution...

Results:

Marginal probability (MP) estimate:

      
Maximum a posteriori (MAP) estimate:

      
Marginal probabilities

Software by David B. Dahl.