No Promoter Left Behind (NPLB): learn de novo promoter architectures from genome-wide transcription start sites

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Abstract

Summary: Promoters have diverse regulatory architectures and thus activate genes differently. For example, some have a TATA-box, many others do not. Even the ones with it can differ in its position relative to the transcription start site (TSS). No Promoter Left Behind (NPLB) is an efficient, organism-independent method for characterizing such diverse architectures directly from experimentally identified genome-wide TSSs, without relying on known promoter elements. As a test case, we show its application in identifying novel architectures in the fly genome.

Availability and implementation: Web-server at http://nplb.ncl.res.in. Standalone also at https://github.com/computationalBiology/NPLB/ (Mac OSX/Linux).

Contact:l.narlikar@ncl.res.in

Supplementary information: Supplementary data are available at Bioinformatics online.

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