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Paleontologists like what Olsen and his colleagues did with their huge footprint database.
To identify possible candidates, we used Patser to scan HSF-bound promoters and introns for matches (Bonferroni corrected p-value<5.6×10−2) to PWMs representing 111 different DNA binding proteins from two databases, Transfac and the Drosophila DNase I Footprint Database.
We repeated these steps to identify matches to all other unique PWMs from TRANSFAC and from the Drosophila DNase I Footprint Database this time counting matches to each matrix in HSF-bound promoters and HSF-bound introns with Bonferroni corrected p-values <5.6×10−2.
Specifically for the characterization of TF binding sites, the information is distributed into different resources: FlyTF is a comprehensive catalog of TFs with DNA-binding properties [ 38], while REDfly, FlyFactorSurvey, and the DNase footprint database are compilations of TFBSs experimentally validated in Drosophila[ 39- 41].
Specialized databases providing a list of sequence specific TF (Adryan and Teichmann, 2006), collections of CRM and TFBS information from literature (Halfon et al., 2008), Drosophila cis-regulatory element database (Narang et al., 2006), DNAse I footprint database (Bergman et al., 2005) and position weight matrices (Sandelin et al., 2004; Wingender et al., 1997) are available.
Similar(55)
During the quarter, the company released its Internet Foundation.2000 product, which helps businesses create e-commerce web sites, and also announced the acquisition of Cloudscape, which makes small-footprint databases that let workers access corporate networks through mobile devices like laptops and handheld PCs.
Then, the bill of quantities (BOQ) and the engineering quota were used along with the established carbon footprint factor database (CFFD) to calculate the carbon footprints (CFs) of the buildings.
Battelle calls these clickstreams, or footprints, the "Database of Intentions".
These techniques and methods will also minimize the actual database "footprint" or space allocation on DASD, while at the same time allowing the model to represent the business and be flexible to those predictable business changes that might occur.
"It wouldn't surprise me if four or five years from now we were having the same conversation about adding footprints" to the database, he said.
This approach is used by ConSite [ 13], which uses ORCA algorithm [ 14] for phylogenetic footprinting and JASPAR database for TFBS sequence identification.
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