PMC:1794230 / 56486-57376 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/1794230","sourcedb":"PMC","sourceid":"1794230","source_url":"https://www.ncbi.nlm.nih.gov/pmc/1794230","text":"Obtaining binding site motif models\nE. coli Crp and PurR binding sites that have been experimentally identified by DNase I footprinting were extracted from the literature and available databases, RegulonDB [47] and DPInteract [48]. The 87 Crp sites (from 65 E. coli intergenic regions) and 22 PurR sites (from 20 E. coli intergenic regions), were aligned using the Gibbs Recursive Sampler [49] specifying palindromic models (total width of 16–24 bp), to generate a PurR motif (Figure 7) and a Crp motif (Figure 1). These figures show both the nucleotide equilibrium and the information content for each position of the motif [9].\nFigure 7 PurR Binding Site Motif. Shown is the PurR motif used to scan for PurR binding sites. The binding site equilibria were calculated from sequence data aligned by the Gibbs Recursive Sampler [49], and were plotted using publicly available software [27].","divisions":[{"label":"title","span":{"begin":0,"end":35}},{"label":"p","span":{"begin":36,"end":629}},{"label":"label","span":{"begin":630,"end":638}}],"tracks":[{"project":"2_test","denotations":[{"id":"17244358-14681419-1689336","span":{"begin":207,"end":209},"obj":"14681419"},{"id":"17244358-9813115-1689337","span":{"begin":227,"end":229},"obj":"9813115"},{"id":"17244358-12824370-1689338","span":{"begin":390,"end":392},"obj":"12824370"},{"id":"17244358-3525846-1689339","span":{"begin":626,"end":627},"obj":"3525846"}],"attributes":[{"subj":"17244358-14681419-1689336","pred":"source","obj":"2_test"},{"subj":"17244358-9813115-1689337","pred":"source","obj":"2_test"},{"subj":"17244358-12824370-1689338","pred":"source","obj":"2_test"},{"subj":"17244358-3525846-1689339","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#e093ec","default":true}]}]}}