Faspad：快速信号通路检测

Faspad: fast signaling pathway detection.

作者信息

Hüffner Falk, Wernicke Sebastian, Zichner Thomas

机构信息

Institut für Informatik, Friedrich-Schiller-Universität Jena, Ernst-Abbe-Platz 2, D-07743 Jena, Germany.

出版信息

Bioinformatics. 2007 Jul 1;23(13):1708-9. doi: 10.1093/bioinformatics/btm160. Epub 2007 Apr 26.

DOI:10.1093/bioinformatics/btm160

PMID:17463016

Abstract

UNLABELLED

Faspad is a user-friendly tool that detects candidates for linear signaling pathways in protein interaction networks based on an approach by Scott et al. (Journal of Computational Biology, 2006). Using recent algorithmic insights, it can solve the underlying NP-hard problem quite fast: for protein networks of typical size (several thousand nodes), pathway candidates of length up to 13 proteins can be found within seconds and with a 99.9% probability of optimality. Faspad graphically displays all candidates that are found; for evaluation and comparison purposes, an overlay of several candidates and the surrounding network context can also be shown.

AVAILABILITY

Faspad is available as free software under the GPL license at http://theinf1.informatik.uni-jena.de/faspad/ and runs under Linux and Windows.

摘要

未标注

Faspad是一个用户友好型工具，它基于Scott等人（《计算生物学杂志》，2006年）的方法，在蛋白质相互作用网络中检测线性信号通路的候选对象。利用最近的算法见解，它能够相当快速地解决潜在的NP难问题：对于典型规模（几千个节点）的蛋白质网络，长度达13个蛋白质的通路候选对象能在数秒内找到，且最优性概率为99.9%。Faspad以图形方式显示所有找到的候选对象；为了评估和比较目的，还可以显示多个候选对象及其周围网络环境的叠加图。