CROSS CHECKER: COMPUTER ASSISTED SCORING OF GENETIC AFLP DATA

Laboratory of Plant Breeding Wageningen University and Research Centre P.O. Box 386 6700 AJ Wageningen The Netherlands

Cross Checker is a freeware software package dedicated to the binary interpretation of DNA fingerprints (AFLP, RFLP and RAPD). Cross Checker provides a computer-assisted version of manual analysis of the gel image, rather than a full automation of this process. Automated fragment and lane detection often gives highly variable results, which necessitates user intervention, for instance to prevent homologous fragments with mobility shifts due to gel artifacts to be interpreted as two independent markers. In Cross Checker, lanes and markers are chosen and defined by the user and drawn with computer assistance. The software will then determine local signals and propose a present/absent fragment scoring for each marker, taking in account the signal range of the fragments of each individual marker. The result of this approach is a package that is capable of marker scoring on gel images of several sources (either autoradiograms or results obtained with phosphor-imagers and fluorescent sequencers). The interpretation procedure of the program was developed with the experimental design of marker genetics in mind, in which the very accurate scoring of a chosen subset of markers on the image is more important than the scoring of all possible markers. Cross Checker is capable of inferring allelic data either with or without parental fingerprints on the same gel image, and exports the segregation data in JoinMap format. Cross Checker is available at: http://www.spg.wau.nl/pv/pub/CrossCheck/