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Nucleic Acids Research Advance Access originally published online on May 17, 2008
Nucleic Acids Research 2008 36(Web Server issue):W470-W474; doi:10.1093/nar/gkn277
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Nucleic Acids Research, 2008, Vol. 36, No. suppl_2 W470-W474
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

Signature, a web server for taxonomic characterization of sequence samples using signature genes

Bas E. Dutilh*, Ying He, Maarten L. Hekkelman and Martijn A. Huynen

Center for Molecular and Biomolecular Informatics/Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands

*To whom correspondence should be addressed. Tel: +31 024 3619797; Fax: +31 024 3619395; Email: dutilh{at}cmbi.ru.nl

Received January 30, 2008. Revised April 14, 2008. Accepted April 26, 2008.

Signature genes are genes that are unique to a taxonomic clade and are common within it. They contain a wealth of information about clade-specific processes and hold a strong evolutionary signal that can be used to phylogenetically characterize a set of sequences, such as a metagenomics sample. As signature genes are based on gene content, they provide a means to assess the taxonomic origin of a sequence sample that is complementary to sequence-based analyses. Here, we introduce Signature (http://www.cmbi.ru.nl/signature), a web server that identifies the signature genes in a set of query sequences, and therewith phylogenetically characterizes it. The server produces a list of taxonomic clades that share signature genes with the set of query sequences, along with an insightful image of the tree of life, in which the clades are color coded based on the number of signature genes present. This allows the user to quickly see from which part(s) of the taxonomy the query sequences likely originate.

Present address: Ying He, VIB Department of Plant Systems Biology, Ghent University, Technologiepark 927, 9052 Gent, Belgium


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