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Nucleic Acids Research, 2003, Vol. 31, No. 13 3712-3715
© 2003 Oxford University Press

Automated Gene Ontology annotation for anonymous sequence data

Steffen Hennig*, Detlef Groth and Hans Lehrach

Max-Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin, Germany

*To whom correspondence should be addressed. Tel: +49 30 8413 1612; Fax: +49 30 8413 1380; Email: hennig{at}molgen.mpg.de
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

Gene Ontology (GO) is the most widely accepted attempt to construct a unified and structured vocabulary for the description of genes and their products in any organism. Annotation by GO terms is performed in most of the current genome projects, which besides generality has the advantage of being very convenient for computer based classification methods. However, direct use of GO in small sequencing projects is not easy, especially for species not commonly represented in public databases. We present a software package (GOblet), which performs annotation based on GO terms for anonymous cDNA or protein sequences. It uses the species independent GO structure and vocabulary together with a series of protein databases collected from various sites, to perform a detailed GO annotation by sequence similarity searches. The sensitivity and the reference protein sets can be selected by the user. GOblet runs automatically and is available as a public service on our web server. The paper also addresses the reliability of automated GO annotations by using a reference set of more than 6000 human proteins. The GOblet server is accessible at http://goblet.molgen.mpg.de.


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