PMID: 8948640Nov 15, 1996Paper

Mapping genes within a YAC by computer-assisted interpretation of partial restriction digestions

Nucleic Acids Research
D C ShieldsA S Whitehead

Abstract

Partial restriction digestion is used to map restriction sites and the location of genes within yeast artificial chromosomes (YACs). Locus-specific probes are hybridised to the partially digested YAC DNA and the fragments to which they hybridise are compared with the pattern of partial digestion products that include each map region. A least squares criterion is presented which allows for error in fragment length determination. This rapidly defines the most likely location of a marker within the restriction map and permits the combination of results from digestions with different restriction enzymes. Approximate confidence intervals may be assigned to gene locations, and tests of goodness-of-fit of the data may be performed. Since the number of erroneously matched fragments increases in proportion to the square of the number of sites, denser maps are not necessarily more informative. Simulations indicate that the optimal number of internal restriction sites given typical experimental error (1% of YAC length) is about five sites; the associated broad support interval (on average one third of YAC length) may be reduced by combining results from different enzyme digestions. Application of a computer implementation of this model to...Continue Reading

References

Sep 1, 1976·Nucleic Acids Research·H O Smith, M L Birnstiel
Jun 1, 1995·Computer Applications in the Biosciences : CABIOS·R M Karp, L A Newberg
Mar 1, 1995·Journal of Medical Microbiology·C A Hart
Mar 1, 1994·Bulletin of Mathematical Biology·S S Skiena, G Sundaram
Jan 1, 1996·Nucleic Acids Research·K H FasmanD T Kingsbury
Jan 1, 1996·Immunogenetics·M T WalshA S Whitehead

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Citations

May 29, 2002·Biochimica Et Biophysica Acta·Hung-Chien Roger ChienWen-Hwei Hsu
May 29, 1998·Biochimica Et Biophysica Acta·J H LeeI S Kong

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