Proteome Analyst -- Transparent High-throughput Protein Annotation: Function, Localization and Custom Predictors
- Duane Szafron, UofA CS
- Russ Greiner, Dept of Computing Science; PI of AICML
- Paul Lu, Department of Computing Science
- David S. Wishart, Departments of Computing Science and Biology, University of Alberta
- Zhiyong Lu
- Brett Poulin, Computing Science
- Roman Eisner
- John Anvik
- Cam Macdonell, Computing Science
Modern sequencing technology permits sequencing of entire genomes, whose gene sequences require annotation. It is too time consuming to predict the properties of each protein sequence manually and to organize the results of many prediction tools by hand. The prediction process must be automated, but the predictions must also be transparent. That is, the rationale for each prediction should be easily examinable by anyone that wishes to use the prediction. Proteome Analyst (PA) is a web-based system for predicting the properties of each protein in a proteome. PA has three interesting features. First, it is a single web-based system that allows the user to select a wide range of analytic tools and automatically apply them to each protein in a proteome. In essence, PA provides one-stop automatic high-throughput analysis. Second, PA has the ability to explain its predictions to users. PA is based on established machine learning techniques, but makes every prediction transparent to its users. Third, PA allows users to create their own transparent custom predictors without programming.
Citation
D. Szafron, R. Greiner, P. Lu, D. Wishart, Z. Lu, B. Poulin, R. Eisner, J. Anvik, C. Macdonell. "Proteome Analyst -- Transparent High-throughput Protein Annotation: Function, Localization and Custom Predictors". Bioinformatics Workshop, August 2003.| Keywords: | Proteome Analyst, machine learning, naive bayes, bioinformatics |
| Category: | In Workshop |
BibTeX
@misc{Szafron+al:Bioinfo-ICML03,
author = {Duane Szafron and Russ Greiner and Paul Lu and David S. Wishart and
Zhiyong Lu and Brett Poulin and Roman Eisner and John Anvik and Cam
Macdonell},
title = {Proteome Analyst -- Transparent High-throughput Protein Annotation:
Function, Localization and Custom Predictors},
Booktitle = {Bioinformatics Workshop (ICML)},
booktitle = {Bioinformatics Workshop},
year = 2003,
}Last Updated: August 16, 2007Submitted by Russ Greiner
