SIFTER
SIFTER: Statistical Inference of Function Through Evolutionary
Relationships
- B.E. Engelhardt, M.I. Jordan, J.R. Srouji, and S.E. Brenner
(2009). Genome-scale phylogenetic function annotation of large and diverse
protein families. Submitted.
- B.E. Engelhardt, M.I. Jordan, and S.E. Brenner (2006). A graphical model for predicting protein molecular
function. Proceedings of the International Conference on Machine Learning
(ICML). [PDF]
- B.E. Engelhardt, M.I. Jordan, K.E. Muratore, and S.E. Brenner (2005). Protein molecular function prediction by Bayesian phylogenomics PLoS Computational Biology, 1, 432-445, 2005. [PDF]
SIFTER Downloadable Code
The newest version of the code (version 1.2), fully described in a recently
submitted paper (please email for draft: bee@compbio.berkeley.edu). This is
still research-quality code, so expect a little work to go into setting it
it. It is still in active development, so if you have any comments, problems,
or feedback, please send me an email (bee@compbio.berkeley.edu).
To set up SIFTER on your computer, please see the README in the top directory,
and to build the files see the readme in the scripts folder. There is a
hypothetical family there as a test family so you can see what all of the
files look like and how output is organized.
Download the newest version of the code here: [SIFTER_1.2]
We also include here the previous version of SIFTER, described in the ICML
paper posted above, for additional files and as reference: [SIFTER_0.3]
Gold-Standard Data Sets
We plan on releasing our gold-standard data sets for all of the data presented
in the most recent paper. In order to do this, an additional paper needs to be
submitted; please email me in the meanwhile to have access to any of this
information.
SIFTER Future Developments
Check back here for a SIFTER server sometime in the next few months!
Barbara
Engelhardt