NAR Molecular Biology Database Collection entry number 231
ACTIVITY, a database on DNA site sequences with known activity magnitudes, measurement systems and sequence-activity relationships under fixed experimental conditions is additionally adapted to applications to the phylogenetic footprints of known sites. To this aim, we have created three resources, ACTIVITY_Reports, ACTIVITY_Tuning, and TFsite_Annotations. For a given site with known sequence-activity relationships, the first database ACTIVITY_Reports accumulates the quantitative data on the impact of the site surrounding, which allows for correct recognition of this site. From this way characterized site-surrounding relationships, the Java applet aimed at precise analysis of phylogenetic footprints of only this known site is automatically generated and stored within the knowledge base ACTIVITY_Tuning. Next, the resulting database TFsite_Annotations documents the Java applet results obtained in the cases of only putative sites of the same type and the same location within the same regulatory region of the homologous gene. The resources enriching the current ACTIVITY release are available at URL=http://util.bionet.nsc.ru/databases/activity.html.
In our previous paper [Nucleic Acids Res, 29(1):284-287] we have developed the database ACTIVITY on DNA sequences with known quantitative activity rates and, thus, provided a hundred cross-tests between various sequence-activity relationships grouped by their protein-targets. All these cross-test results indicated that, for a given protein-binding site, the basic impact of the site core into sequence-activity relationships is invariant, whereas the modulating impact of the site surround is not. Since, with unpredictable surrounding-dependencies, it was not clear, what might be used for applying sequence-activity relationships in practice, the available components of our database ACTIVITY were slightly extended. To address this formidable challenge, our guesswork is that for two sites of the same type and at the same location within the same regions of homologous genes, surrounding-dependencies of sequence-activity relationships must be the most similar due to their common evolution origin. That is why the main idea of our recent developments was to precisely focus them on only the phylogenetic footprints of the protein-binding sites with known sequence-activity relationships. Therefore, in this work we have developed three resources, ACTIVITY_Reports, ACTIVITY_Tuning, and TFsite_Annotations. For a given site with known sequence-activity relationships, the first database ACTIVITY_Reports accumulates the quantitative data on the impact of the site surrounding, which allows for correct recognition of this site. From this way characterized site-surrounding relationship, the Java applet aimed at precise analysis of phylogenetic footprints of only this known site is automatically generated and stored within the next knowledge base ACTIVITY_Tuning. So that, the resulting database TFsite_Annotations documents the Java applet results obtained in the cases of only putative sites of the same type and the same location within the same regulatory region of homologous gene. The resources enriching the present ACTIVITY release are available at URL=http://util.bionet.nsc.ru/databases/activity.html
The work is supported by Russian Foundation for Basic Research, 01-04-49860 and 02-04-49485.
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Category: Nucleotide Sequence Databases
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