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SITECON: a tool for detecting conservative conformational and physicochemical properties in transcription factor binding site alignments and for site recognition

D. Y. Oshchepkov, E. E. Vityaev, D. A. Grigorovich, E. V. Ignatieva, T. M. Khlebodarova
2004 Nucleic Acids Research  
The web resource SITECON is designed to detect conservative conformational and physicochemical properties in transcription factor binding sites, contains a knowledge base of conservative properties for  ...  .100 high-quality sample sites and allows for recognition of potential transcription factor binding sites based on conservative properties from both the knowledge base and the results of analysis of a  ...  A. Afonnikov for fruitful discussion of the study and G. B. Chirikova for assistance in translation. The work was supported by the Russian  ... 
doi:10.1093/nar/gkh474 pmid:15215382 pmcid:PMC441612 fatcat:crkwusd4b5cjvbr43zexggi52i

Guide to Genome-Wide Bacterial Transcription Factor Binding Site Prediction Using OmpR as Model [chapter]

Phu Vuong, Rajeev Misr
2011 Selected Works in Bioinformatics  
Even though a TF often regulates multiple genes and the binding sites in the promoters of these genes show variations, certain conformational and physicochemical properties are conserved among these sites  ...  The user picks a bacterial genome from a list of over 110 and supplies a set of aligned binding site sequences for the transcription factor.  ... 
doi:10.5772/24321 fatcat:pksnry4cf5fsjhogx43p6hdy54

Molecular characterization of vernalization loci VRN1 in wild and cultivated wheats

Kseniya A Golovnina, Elena Kondratenko, Alexander G Blinov, Nikolay P Goncharov
2010 BMC Plant Biology  
Some transcription factor recognition sites including hybrid C/G-box for TaFDL2 protein known as the VRN1 gene upregulator were predicted inside the variable region.  ...  At the same time, the duplication of the promoter region was observed in A genomes of polyploid species.  ...  Authors' contributions KG designed the study, carried out the molecular and bioinformatics experiment, drafted the manuscript. EYK and NPG carried out greenhouse and genetic analysis.  ... 
doi:10.1186/1471-2229-10-168 pmid:20699006 pmcid:PMC3095301 fatcat:4lc3ysjxsnagni2wmrtypxkjqy