Fang Fei, Blanchette Mathieu
McGill Centre for Bioinformatics, 3775 University St, Montréal, Québec, Canada, H3A 2B4.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W617-20. doi: 10.1093/nar/gkl123.
FootPrinter3 is a web server for predicting transcription factor binding sites by using phylogenetic footprinting. Until now, phylogenetic footprinting approaches have been based either on multiple alignment analysis (e.g. PhyloVista, PhastCons), or on motif-discovery algorithms (e.g. FootPrinter2). FootPrinter3 integrates these two approaches, making use of local multiple sequence alignment blocks when those are available and reliable, but also allowing finding motifs in unalignable regions. The result is a set of predictions that joins the advantages of alignment-based methods (good specificity) to those of motif-based methods (good sensitivity, even in the presence of highly diverged species). FootPrinter3 is thus a tool of choice to exploit the wealth of vertebrate genomes being sequenced, as it allows taking full advantage of the sequences of highly diverged species (e.g. chicken, zebrafish), as well as those of more closely related species (e.g. mammals). The FootPrinter3 web server is available at: http://www.mcb.mcgill.ca/~blanchem/FootPrinter3.
FootPrinter3是一个通过系统发育足迹法预测转录因子结合位点的网络服务器。到目前为止，系统发育足迹法要么基于多序列比对分析（如PhyloVista、PhastCons），要么基于基序发现算法（如FootPrinter2）。FootPrinter3整合了这两种方法，在有可用且可靠的局部多序列比对块时加以利用，同时也允许在无法比对的区域中寻找基序。结果是一组预测，它结合了基于比对方法的优点（高特异性）和基于基序方法的优点（高灵敏度，即使在存在高度分化物种的情况下）。因此，FootPrinter3是利用正在测序的大量脊椎动物基因组的首选工具，因为它能够充分利用高度分化物种（如鸡、斑马鱼）以及亲缘关系较近物种（如哺乳动物）的序列。FootPrinter3网络服务器可通过以下网址访问：http://www.mcb.mcgill.ca/~blanchem/FootPrinter3 。
