LASAGNA-Search 2.0: integrated transcription factor binding site search and visualization in a browser
LASAGNA-Search 2.0: integrated transcription factor binding site search and visualization in a browser
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DOI：
10.1093/bioinformatics/btu115
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发表时间：
2014-07-01
期刊：
影响因子：
5.8
通讯作者：
Huang, Chun-Hsi
中科院分区：
文献类型：
--
作者：
Lee, Chih;Huang, Chun-Hsi
LASAGNA-Search 2.0是一个用于转录因子（TF）结合位点搜索和可视化的集成网络工具。该工具基于LASAGNA（核苷酸关联引导的长度感知位点比对）算法。它消除了手动TF模型收集和启动子序列检索。搜索结果可以在本地或加州大学圣克鲁斯基因组浏览器中可视化。基于搜索结果的基因调控网络推理提供了另一种可视化方式。TF和靶基因的列表是用户开始使用该工具所需的全部。LASAGNA-Search 2.0目前提供了1792个TF模型，并支持15个物种在加州大学圣克鲁斯基因组浏览器中进行自动启动子检索和可视化。它是为非生物信息学家设计的用户友好的工具，适合研究和教学。我们描述了自初始版本以来所做的重要更改。可用性和实施：LASAGNA-Search 2.0免费提供，无需在www.example.com注册。
LASAGNA-Search 2.0 is an integrated webtool for transcription factor (TF) binding site search and visualization. The tool is based on the LASAGNA (Length-Aware Site Alignment Guided by Nucleotide Association) algorithm. It eliminates manual TF model collection and promoter sequence retrieval. Search results can be visualized locally or in the University of California Santa Cruz Genome Browser. Gene regulatory network inference based on the search results offers another way of visualization. A list of TFs and target genes is all a user needs to start using the tool. LASAGNA-Search 2.0 currently offers 1792 TF models and supports 15 species for automatic promoter retrieval and visualization in the University of California Santa Cruz Genome Browser. It is a user-friendly tool designed for non-bioinformaticians and is suitable for research and teaching. We describe important changes made since the initial release. Availability and implementation: LASAGNA-Search 2.0 is freely available without registration at http://biogrid.engr.uconn.edu/lasagna_search/.