PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood.
Publication year
2009Number of pages
8 p.
Source
Nucleic Acids Research, 37, Database issue, (2009), pp. D731-737ISSN
Publication type
Article / Letter to editor
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Organization
Bioinformatics
CMBI
Former Organization
Bioinformatics (umcn)
Journal title
Nucleic Acids Research
Volume
vol. 37
Issue
iss. Database issue
Page start
p. D731
Page end
p. 737
Subject
Bioinformatics; NCMLS 7: Chemical and physical biologyAbstract
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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