Van Hellemont Ruth, Monsieurs Pieter, Thijs Gert, de Moor Bart, Van de Peer Yves, Marchal Kathleen
ESAT-SCD, KU Leuven, Kasteelpark Arenberg 10, 3001 Leuven-Heverlee, Belgium.
Genome Biol. 2005;6(13):R113. doi: 10.1186/gb-2005-6-13-r113. Epub 2005 Dec 30.
Although proven successful in the identification of regulatory motifs, phylogenetic footprinting methods still show some shortcomings. To assess these difficulties, most apparent when applying phylogenetic footprinting to distantly related organisms, we developed a two-step procedure that combines the advantages of sequence alignment and motif detection approaches. The results on well-studied benchmark datasets indicate that the presented method outperforms other methods when the sequences become either too long or too heterogeneous in size.
尽管系统发育足迹法在识别调控基序方面已被证明是成功的，但它仍然存在一些缺点。为了评估这些困难（在将系统发育足迹法应用于亲缘关系较远的生物体时最为明显），我们开发了一种两步法，该方法结合了序列比对和基序检测方法的优点。在经过充分研究的基准数据集上的结果表明，当序列变得过长或大小差异过大时，所提出的方法优于其他方法。
