Project 1: The Mouse Brain Library Project 2: Internet Microscopy (iScope) Project 3: Neurocartographer and Segmentation of the MBL Project 4: The Neurogenetics Tool Box


















Principal Investigator/Program Director Williams, Robert W.


Existing Map Manager software

The Map Manager family of genetic mapping software consists of four programs, the latest of which will be released before the start of this program project. These programs have been developed with support from the National Human

Genome Research Institute and the Rockefeller Foundation. The programs and user manuals have been distributed without charge.

The first two existing programs are described fully in the user manuals for Map Manager QT included in the appendix. Map Manager Classic maps Mendelian loci in recombinant inbred lines, backcrosses, and intercrosses with codominant markers. It was started in 1988 as a program to manage and use the rapidly growing volume of data from mouse recombinant inbred lines (Manly and Elliott 1991) , and additional functions were added later (Manly 1993) . Map Manager Classic runs only under Mac OS and is written in Pascal. Map Manager QT, an augmented version of Map Manager Classic, includes functions for the detection and mapping of QTLs by regression-based single-locus association, simple interval mapping, and composite interval mapping. It also provides permutation tests for establishing empirical significance levels for putative QTLs. Map Manager QT has been used extensively in the preliminary work leading to this proposal.

Map Manager XP is a mapping program for Mendelian traits, but unlike Map Manager Classic, it accepts dominant alleles and populations in which adjacent loci show different segregation patterns. It is written in C++ and, more important, uses a commercial portable library called XVT. This allows the code, with minor modifications, to be compiled for a variety of machines and/or operating systems. Map Manager QTX, an augmented version of Map Manager XP with the same functions for detection and mapping of QTLs as Map Manager QT, will handle additional types of mapping populations, including advanced backcrosses and advanced intercrosses such as the G10 intercross described in the Genotyping and Mouse Colony Core. The analysis routines in Map Manager QTX will be adapted for use in the NTB. The first version of Map Manager QTX will be released early in 2000. In addition to providing code for the Web-based mapping functions proposed here, Map Manager QTX will itself be used by members of this program project.



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