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Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W470-4. doi: 10.1093/nar/gkn277. Epub 2008 May 17.

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

Author information

1
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. dutilh@cmbi.ru.nl

Abstract

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.

PMID:
18487625
PMCID:
PMC2447722
DOI:
10.1093/nar/gkn277
[Indexed for MEDLINE]
Free PMC Article

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