Skip Navigation



Nucleic Acids Research Advance Access published online on May 17, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn277
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (2519K) Freely available
Right arrow Screen PDF (366K) Freely available
Right arrowOA All Versions of this Article:
36/suppl_2/W470    most recent
gkn277v2
gkn277v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Dutilh, B. E.
Right arrow Articles by Huynen, M. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Dutilh, B. E.
Right arrow Articles by Huynen, M. A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 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.

Web Server Issue

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


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
S. Mitra, B. Klar, and D. H. Huson
Visual and statistical comparison of metagenomes
Bioinformatics, August 1, 2009; 25(15): 1849 - 1855.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.