Use of mutation spectra analysis software

The study and comparison of mutation(al) spectra is an important problem in molecular biology, because these spectra often reflect on important featur es of mutations and their fixation. Such features include the interaction o f DNA with various mutagens, the function of repair/replication enzymes, an d properties of target proteins. It is known that mutability varies signifi cantly along nucleotide sequences, such that mutations often concentrate at certain positions, called "hotspots," in a sequence. In this paper, we dis cuss in detail two approaches for mutation spectra analysis: the comparison of mutation spectra with a HG-PUBL program, (FTP: sunsite.unc.edu/pub/acad emic/ biology/dna-mutations/hyperg) and hotspot prediction with the CLUSTER M program (www.itba.mi.cnr.it/webmutation; ftp.bionet.nsc.ru/pub/biology/db ms/clusterm.zip). Several other approaches for mutational spectra analysis, such as the analysis of a target protein structure, hotspot context reveal ing, multiple spectra comparisons, as well as a number of mutation database s are briefly described. Mutation spectra in the lacl gene of E. coli and t he human p53 gene are used for illustration of various difficulties of such analysis. Hum Mutat 17:83-102, 2001. (C) 2001 Wiley-Liss, Inc.