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Bioinformatics Advance Access originally published online on August 12, 2008
Bioinformatics 2008 24(20):2393-2394; doi:10.1093/bioinformatics/btn394
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Protein function prediction and annotation in an integrated environment powered by web services (AFAWE)

Anika Jöcker , Fabian Hoffmann , Andreas Groscurth and Heiko Schoof *

Plant Computational Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany

*To whom correspondence should be addressed.


  Abstract

Summary: Many sequenced genes are mainly annotated through automatic transfer of annotation from similar sequences. Manual comparison of results or intermediate results from different tools can help avoid wrong annotations and give hints to the function of a gene even if none of the automated tools could return any result.

AFAWE simplifies the task of manual functional annotation by running different tools and workflows for automatic function prediction and displaying the results in a way that facilitates comparison. Because all programs are executed as web services, AFAWE is easily extensible and can directly query primary databases, thereby always using the most up-to-date data sources. Visual filters help to distinguish trustworthy results from non-significant results. Furthermore, an interface to add detailed manual annotation to each gene is provided, which can be displayed to other users.

Availability: AFAWE is available at http://bioinfo.mpiz-koeln.mpg.de/afawe/

Contact: afawe-admin{at}mpiz-koeln.mpg.de

Supplementary information: SIFTER pipeline (S1), AFAWE tutorial (S2).

Associate Editor: Burkhard Rost

Received on April 28, 2008; revised on July 16, 2008; accepted on July 26, 2008

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