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Human p53, human hprt, rodent lacI and rodent lacZ databases


NAR Molecular Biology Database Collection entry number 134

Database Description

Databases and software applications for the analysis of DNA mutations at the human p53 gene, the human hprt gene and both the rodent transgenic lacI and lacZ locus have been created. The number of mutations in each database is as follows: p53 - 5,900; hprt - 2,500; lacI - approximately 1,500 transgenic and 8,000 bacterial; lacZ - approximately 200. The databases themselves are stand-alone dBASE files and the software for analysis of the databases runs on IBM-compatible computers running Microsoft Windows. Each database has a separate software analysis program. The software created for these databases permit the filtering, ordering, report generation and display of information in the database. In addition, a significant number of routines have been developed for the analysis of single base substitutions. The databases and software can be obtained at: http://metalab.unc.edu/dnam/mainpage.html Each database is in the dBASE format and is present as a stand-alone file. Information common to all databases includes (i) base position, (ii) the nature of the mutation, (iii) amino acid position, (iv) wt and mutant amino acid, (v) the local sequence around a mutation and (vi) literature citation. Information specific to the p53 database includes (i) cancer type, (ii) cell origin (tumor, cell line, etc.) and (iii) loss of heterozygosity. Data particular to the hprt database includes (i) mutagen, (ii) dose, (iii) background and induced mutation frequencies, (iv) information whether the mutant was generated in vivo or in vitro, (v) mRNA splicing information for mutants affecting splicing and (vi) cell type. Data contained in the lacZ transgenic database includes (i) dose, (ii) time from last treatment to animal sacrifice, (iii) supplier, species, strain, sex and age of animal, (iv) the organs selected for mutation analysis, (v) the mutant fraction in each organ, (vi) the total PFU analyzed and (vii) the plaque color. Data in the lacI database are very similar to the lacZ database. A significant number of routines have been developed for the analysis of single base substitutions, including programs to (i) determine if two mutational spectra are different, (ii) display mutable amino acids in the protein, (iii) determine if mutations show a DNA strand bias, (iv) determine the frequency of transitions and transversions, (v) display the number and kind of mutations observed at each base in the coding region and (vi) perform nearest neighbor analysis. For genes with exons, a routine will display the number of mutations and mutable sites in each exon. Graphics displays are available for mutated amino acids and for mutational spectra representation.

Subcategory: Cancer gene databases

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