Batch extraction and analysis of ds-regulatory regions (BEARR) (1) is a web-based tool devised with biologists as end users for assisting them in the regulatory sequence analysis surrounding their genes of interest. It was designed for high-throughput motif searches around regulatory regions of genes. BEARR can identify putative transcription factor binding sites of a large set of genes, such as those coming from microarray studies or other genome-wide investigations. The system contains two main parts: the regulatory region sequence extraction module and the sequence analysis module.

From: Methods in Molecular Biology, vol. 338: Gene Mapping, Discovery, and Expression: Methods and Protocols Edited by: M. Bina © Humana Press Inc., Totowa, NJ

in fact forms a cycle, depicting the iterative nature of the process.

The following sections discuss problem abstraction and question formulation prior to running analysis with BEARR, describe how to perform an analysis, expound what can be expected from the analysis, explore features of BEARR, and suggest potential additional analyses.

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