LASAGNA-Search 2.0: integrated transcription factor binding site search and visualization in a browser | Zendy

Chih Lee | Zendy; Chun-Hsi Huang | Zendy

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LASAGNA-Search 2.0: integrated transcription factor binding site search and visualization in a browser

Author(s) -

Chih Lee,

Chun-Hsi Huang

Publication year - 2014

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btu115

Subject(s) - genome browser , visualization , inference , computational biology , transcription factor , computer science , genome , information retrieval , dna binding site , interactive visualization , transcription (linguistics) , gene , biology , world wide web , data mining , promoter , genomics , genetics , artificial intelligence , gene expression , linguistics , philosophy

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.

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