PIPA: A Tool for Protein Function Annotation
Author Information
Author(s): Yu Chenggang, Zavaljevski Nela, Desai Valmik, Johnson Seth, Stevens Fred J, Reifman Jaques
Primary Institution: Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Ft. Detrick, MD, USA
Hypothesis
An integrated pipeline can improve the accuracy of genome-wide protein function annotation by combining multiple resources.
Conclusion
PIPA provides automated genome-wide protein function annotation based on reconciled predictions from multiple resources.
Supporting Evidence
- PIPA integrates 16 programs/databases for protein function prediction.
- CatFam, a database within PIPA, achieves over 99% precision in enzyme function predictions.
- PIPA's consensus algorithm improves precision of GO annotations by up to 8%.
Takeaway
PIPA is a computer program that helps scientists figure out what proteins do by using information from many different sources.
Methodology
PIPA integrates multiple programs and databases to annotate protein functions, using algorithms for profile generation, ontology mapping, and consensus annotation.
Potential Biases
Potential false-positive predictions from integrated methods based on short motifs.
Limitations
PIPA's predictions are currently limited to methods based on sequence homology, which may lead to false positives.
Digital Object Identifier (DOI)
Want to read the original?
Access the complete publication on the publisher's website