Statistical and computational challenges in physical mapping
One of the great success stories of modern molecular genetics has been the ability of biologists to isolate and characterize the genes responsible for serious inherited diseases like Huntington`s disease, cystic fibrosis, and myotonic dystrophy. Instrumental in these efforts has been the construction of so-called {open_quotes}physical maps{close_quotes} of large regions of human chromosomes. Constructing a physical map of a chromosome presents a number of interesting challenges to the computational statistician. In addition to the general ill-posedness of the problem, complications include the size of the data sets, computational complexity, and the pervasiveness of experimental error. The nature of the problem and the presence of many levels of experimental uncertainty make statistical approaches to map construction appealing. Simultaneously, however, the size and combinatorial complexity of the problem make such approaches computationally demanding. In this paper we discuss what physical maps are and describe three different kinds of physical maps, outlining issues which arise in constructing them. In addition, we describe our experience with powerful, interactive statistical computing environments. We found that the ability to create high-level specifications of proposed algorithms which could then be directly executed provided a flexible rapid prototyping facility for developing new statistical models and methods. The ability to check the implementation of an algorithm by comparing its results to that of an executable specification enabled us to rapidly debug both specification and implementation in an environment of changing needs.
- Research Organization:
- Lawrence Livermore National Lab., CA (United States)
- Sponsoring Organization:
- USDOE, Washington, DC (United States); National Science Foundation, Washington, DC (United States)
- DOE Contract Number:
- W-7405-ENG-48
- OSTI ID:
- 10103388
- Report Number(s):
- UCRL-JC-117919; CONF-9406290-1; ON: DE95003658; TRN: 95:000459
- Resource Relation:
- Conference: 26. symposium on the interface: computer science and statistics,Triangle Park, NC (United States),15-18 Jun 1994; Other Information: PBD: Jun 1994
- Country of Publication:
- United States
- Language:
- English
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