Hulsen Tim, Groenen Peter M A, de Vlieg Jacob, Alkema Wynand
Computational Drug Discovery, CMBI, NCMLS, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500 HB Nijmegen, The Netherlands.
Nucleic Acids Res. 2009 Jan;37(Database issue):D731-7. doi: 10.1093/nar/gkn645. Epub 2008 Oct 2.
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.
系统发育模式展示了来自不同物种的一组完整基因组中某些基因的存在或缺失情况。它们还可用于确定仅在某些进化分支中出现的基因集。此前，我们展示了一个名为PhyloPat的数据库，它允许使用系统发育模式查询完整的Ensembl基因数据库。在此，我们描述了PhyloPat的一个更新版本，它可以通过改进的网络服务器进行查询。我们使用单连锁聚类算法，利用Ensembl v49提供的所有直系同源关系创建了241,697个系统发育谱系。PhyloPat提供了使用二元系统发育模式或正则表达式进行查询的可能性，或者通过39个纳入物种的系统发育树进行查询。用户还可以输入Ensembl、EMBL、EntrezGene或HGNC ID列表，以检查任何基因属于哪个系统发育谱系。HTML输出中已包含指向FatiGO网络界面的链接。对于每个基因，可以查看染色体上周围的基因，这些基因根据其系统发育谱系进行了颜色编码，以及每个谱系的肽序列的FASTA文件。此外，还包括了普遍存在、多物种存在、寡物种存在和反相关基因的列表。PhyloPat可在http://www.cmbi.ru.nl/phylopat免费获取。
