COMPUTERIZED ANALYSIS OF RESTRICTION-FRAGMENT-LENGTH-POLYMORPHISM PATTERNS - COMPARATIVE-EVALUATION OF 2 COMMERCIAL SOFTWARE PACKAGES

Two computerized restriction fragment length polymorphism pattern anal ysis systems, the BioImage system and the GelCompar system (Molecular Analyst Fingerprinting Plus in the United States), were compared. The two systems use different approaches to compare patterns from differen t gels, In GelCompar, a standard reference pattern in one gel is used to normalize subsequent gels containing lanes with the same reference pattern, In BioImage, the molecular sizes of the fragments are calcula ted from size standards present in each gel, The molecular size estima tes obtained with the two systems for 12 restriction fragments of phag e lambda were between 97 and 10% of their actual sizes, with a standar d deviation of less than 1% of the average estimated size for most fra gments. At the window sizes used for analysis, the GelCompar system pe rformed somewhat better than BioImage in identifying visually identica l patterns generated by electrophoretic separation of HhaI-restricted DNA of Listeria monocytogenes. Both systems require the user to make c ritical decisions in the analysis, It is very important to visually ve rify that the systems are finding all hands in each lane and that no a rtifacts are being detected; both systems allow manual editing. It is also important to verify results obtained in the pattern matching or c lustering portions of the analysis.