title: Promoter classifier: software package for promoter database analysis.
abstract: Promoter Classifier is a package of seven stand-alone Windows-based C++ programs allowing the following basic manipulations with a set of promoter sequences: (i) calculation of positional distributions of nucleotides averaged over all promoters of the dataset; (ii) calculation of the averaged occurrence frequencies of the transcription factor binding sites and their combinations; (iii) division of the dataset into subsets of sequences containing or lacking certain promoter elements or combinations; (iv) extraction of the promoter subsets containing or lacking CpG islands around the transcription start site; and (v) calculation of spatial distributions of the promoter DNA stacking energy and bending stiffness. All programs have a user-friendly interface and provide the results in a convenient graphical form. The Promoter Classifier package is an effective tool for various basic manipulations with eukaryotic promoter sequences that usually are necessary for analysis of large promoter datasets. The program Promoter Divider is described in more detail as a representative component of the package.
authors.affiliation: Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA.
authors.forename: Naum I
authors.initials: NI
authors.lastname: Gershenzon
authors.forename: Ilya P
authors.initials: IP
authors.lastname: Ioshikhes
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D003201:Computers; D018899:CpG Islands; D019992:Databases as Topic; D030561:Databases, Nucleic Acid; D020407:Internet; D008969:Molecular Sequence Data; D011381:Programming Languages; D011401:Promoter Regions, Genetic; D012045:Regulatory Sequences, Nucleic Acid; D016415:Sequence Alignment; D012984:Software; D035581:Transcription Factor TFIIB / Q000235:genetics
chemical_list: D035581:Transcription Factor TFIIB