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Nucleic Acids Research Advance Access originally published online on October 2, 2008
Nucleic Acids Research 2009 37(Database issue):D731-D737; doi:10.1093/nar/gkn645
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Nucleic Acids Research, 2009, Vol. 37, Database issue D731-D737
© 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.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood

Tim Hulsen1,*, Peter M. A. Groenen2, Jacob de Vlieg1,2 and Wynand Alkema2

1Computational Drug Discovery (CDD), CMBI, NCMLS, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500 HB Nijmegen and 2Department of Molecular Design and Informatics, Schering-Plough, Molenstraat 110, 5340 BH Oss, The Netherlands

*To whom correspondence should be addressed. Tel: +31 412 668305; Fax: +31 412 662553; Email: t.hulsen{at}cmbi.ru.nl

Received August 12, 2008. Revised September 17, 2008. Accepted September 17, 2008.

Phylogenetic patterns show the presence or absence of certain genes in a set of full genomes derived from different species. They can also be used to determine sets of genes that occur only in certain evolutionary branches. Previously, we presented a database named PhyloPat which allows the complete Ensembl gene database to be queried using phylogenetic patterns. Here, we describe an updated version of PhyloPat which can be queried by an improved web server. We used a single linkage clustering algorithm to create 241 697 phylogenetic lineages, using all the orthologies provided by Ensembl v49. PhyloPat offers the possibility of querying with binary phylogenetic patterns or regular expressions, or through a phylogenetic tree of the 39 included species. Users can also input a list of Ensembl, EMBL, EntrezGene or HGNC IDs to check which phylogenetic lineage any gene belongs to. A link to the FatiGO web interface has been incorporated in the HTML output. For each gene, the surrounding genes on the chromosome, color coded according to their phylogenetic lineage can be viewed, as well as FASTA files of the peptide sequences of each lineage. Furthermore, lists of omnipresent, polypresent, oligopresent and anticorrelating genes have been included. PhyloPat is freely available at http://www.cmbi.ru.nl/phylopat.


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