System to store DNA physical properties profiles with application to the promoters of Escherichia coli
Temlyakova E.A., Dzhelyadin T.R., Kamzolova S.G., Sorokin A.A.
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Database to store, search and retrieve DNA physical properties profiles has been developed and its use for analysis of E. coli promoters has been demonstrated. Unique feature of the database is in its ability to handle whole profile as single internal object type in a way similar to integers or character strings. To demonstrate utility of such database it was populated with data of 1227 known promoters, their nucleotide sequence, profile of electrostatic potential, transcription factor binding sites. Each promoter is also connected to all genes, whose transcription is controlled by that promoter. Content of the database is available for search via web interface. Source code of profile datatype and library to work with it from R/Bioconductor are available from the internet, dump of the database is available from authors by request.

Keywords: E. coli, electrostatic potential of DNA, database, signal analysis
Citation in English: Temlyakova E.A., Dzhelyadin T.R., Kamzolova S.G., Sorokin A.A.
System to store DNA physical properties profiles with application to the promoters of Escherichia coli
// Computer Research and Modeling, 2013, vol. 5, no. 3, pp. 443-450
Citation in English: Temlyakova E.A., Dzhelyadin T.R., Kamzolova S.G., Sorokin A.A.
System to store DNA physical properties profiles with application to the promoters of Escherichia coli
// Computer Research and Modeling, 2013, vol. 5, no. 3, pp. 443-450
DOI: 10.20537/2076-7633-2013-5-3-443-450
URL: http://crm-en.ics.org.ru/journal/article/2029/
Creative Commons License This work is licensed under a Creative Commons Attribution-NoDerivs 3.0 Unported License.
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