The Protein Function Prediction (PFP) pipeline is a Cytoscape plugin which offers a protein annotation service along with visualization of the annotation process. The protein annotation algorithm is based on the analysis of protein interaction network (PIN) plus the integration of heterogeneous data extracted from different external databases. The annotation scheme is tested for proteins of the Homo sapiens and Saccharomyces cerevisiae species. The plugin also provides a detailed visualization aid of the annotation process in Gene Ontology (GO).
Developers
How to cite PFP-PIPELINE
The SysBio development team has invested a lot of time and effort in creating PFP-PIPELINE as it is today. Please give credit where credit is due and cite PFP-PIPELINE when you use it for your research activities.
PFP-PIPELINE can be cited through this papers:
H. U. Rehman, A. Benso, S. Di Carlo, G. Politane, A. Savino and P. Suravajhala, “Combining homolog and motif similarity data with Gene Ontology relationships for protein function prediction,” Bioinformatics and Biomedicine (BIBM), 2012 IEEE International Conference on, Philadelphia, PA, 2012, pp. 1-4.
doi: 10.1109/BIBM.2012.6392719
BibTEX
@INPROCEEDINGS{6392719,
author={H. U. Rehman and A. Benso and S. Di Carlo and G. Politane and A. Savino and P. Suravajhala},
booktitle={Bioinformatics and Biomedicine (BIBM), 2012 IEEE International Conference on},
title={Combining homolog and motif similarity data with Gene Ontology relationships for protein function prediction},
year={2012},
pages={1-4},
keywords={bioinformatics;ontologies (artificial intelligence);proteomics;Protein Protein Interactions;Saccharomyces Cerevisiae;biochemical function;gene ontology relationship;homolog similarity data;hypothetical proteins annotation;motif similarity data;prediction accuracy;protein function prediction;Accuracy;Context;Databases;Ontologies;Protein engineering;Proteins;Function Prediction;Gene Ontology;Protein Interaction Network;Protein motifs},
doi={10.1109/BIBM.2012.6392719},
month={Oct},}
Downloads
Download the PFP-Pipeline JAR File
Download the PFP-Pipeline Source Code