Abstract
A major challenge in systems biology is to discover and reconstruct the cis-regulatory networks through which the expression of genes is controlled. Even though a variety of sequences have been shown to interact with the transcription factors that bind DNA, extensive work is needed to discover and classify regulatory “codes” and to elucidate the role played by the sequence context of genomic DNA in the regulation of genes. Databases of sequence elements extracted from regulatory regions may facilitate this process. This report provides a Toolkit and instructions for creating a database for collecting and analyzing 9-base elements (9-mers) from a large collection of DNA sequences. A reference set consisting of all possible 9-mers is included for extracting potential control elements, irrespective of their orientation and order in DNA.
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Wyss, P., Lazarus, S.A., Bina, M. (2006). A Program Toolkit for the Analysis of Regulatory Regions of Genes. In: Bina, M. (eds) Gene Mapping, Discovery, and Expression. Methods in Molecular Biology, vol 338. Humana Press. https://doi.org/10.1385/1-59745-097-9:135
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DOI: https://doi.org/10.1385/1-59745-097-9:135
Publisher Name: Humana Press
Print ISBN: 978-1-58829-575-0
Online ISBN: 978-1-59745-097-3
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