Restriction Site Mapping is one of the interesting tasks in Computational Biology. A DNA strand can be thought of as a string on the letters A, T, C, and G. When a particular restriction enzyme is added to a DNA solution, the DNA is cut at particular restriction sites. The goal of the restriction site mapping is to determine the location of every site for a given enzyme. In partial digest metho...

We previously developed a cladistic approach to identify subsets of haplotypes defined by restriction endonuclease mapping or DNA sequencing that are associated with significant phenotypic deviations. Our approach was limited to segments of DNA in which little recombination occurs. In such cases, a cladogram can be constructed from the restriction site or sequence data that represents the evolu...

A computer algorithm for restriction-site mapping consists of a generator of partial maps and a consistency checker. This paper examines consistency checking and argues that a method based on separation theory extracts the maximum amount of information from fragment lengths in digest data. It results in the minimum number of false maps being generated.

This paper presents a trie data structure for fast approximate matching of DNA fragments in a large scale restriction mapping project. It analyzes several parameters that aaect the performance of the data structure and brieey explores strategies on how it might be used and how to proceed in the initial stages of potential algorithms for mapping. The paper then reports on experimental results an...

UNLABELLED Restriction endonucleases are indispensable tools in molecular biology and biotechnology. Type II restriction endonucleases are part of restriction modification systems. DNA fragment extraction and restriction mapping are the basis for several biotechnological activities. WebFARM is a server application for identifying restriction endonuclease recognition sites and to give informatio...

Hibbett, D. S., and M. J. Donoghue. 1998. Integrating phylogenetic analysis and classification in fungi. Mycologia 90:347–356. Hibbett, D. S., and Thorn, R.G. 2001. Basidiomycota: Homobasidiomycetes. Pages 121–168 in The Mycota VII, systematics and evolution, Part B (D. J. McLaughlin, E. G. McLaughlin, and P. A. Lemke, eds.) Springer Verlag, Berlin. Hopple, J. S., Jr., and R. Vilgalys. 1994. Ph...

Accurate identification of Alternaria spp. is dependent upon the production of diagnostic morphological characters under defined cultural conditions and the proper assessment of character variation. This process is often compromised by variation in laboratory facilities and technical expertise. To assist taxon identification and phylogenetic studies, restriction site information from the interg...

During senescence in Podospora anserina, specific gene regions of the mitochondrial genome are excised and amplified. The most prevalent, termed alpha-event senDNA, is a 2600 bp circular molecule which is excised from the contiguous Hae III fragments 23,14 region of the mitochondrial DNA restriction map. We have cloned alpha-DNA plasmid from races s+ and A+ as well as the genomic fragments Hae ...