Bi-dimensional scaling map (BDS-Map): an approach for building large genetic maps

Motivation: The approaches usually used for building large genetic maps consist of dividing the marker set into linkage groups and provide local orders that can be tested by multi-point linkage analysis. To deal with the limitations of these approaches, a strategy taking the marker set into account globally is defined. Results: The paper presents a new approach called 'Bi-Dimensional Scaling Map (BDS-Map) for inferring marker orders and distances in genetic maps based on the use of an additional dimension orthogonal to the map into which markers are projected. Dynamical forces based on a two-point analysis are applied to tend to optimize the marker locations in space. The efficiency of the approach is exemplified on real data (16 and 70 markers on chromosomes 6 and 2, respectively) and simulated data (50 maps of 70 markers). Availability: The package called ANGE (ANalyse du GE-nome), including both the program BDS-Map and the system allowing the database management, is available on request from the authors. Contact: E-mail:hazout@urbb.jussieu.fr