A SOFTWARE SYSTEM FOR DATA-ANALYSIS IN AUTOMATED DNA-SEQUENCING

Software for gel image analysis and base-calling in fluorescence-based sequencing consisting of two primary programs, BaseFinder and Gellmag er; is described. BaseFinder is a framework for trace processing, anal ysis, and base-calling, BaseFinder is highly extensible, allowing the addition of trace analysis and processing modules without recompilatio n. Powerful scripting capabilities combined with modularity and multil ane handling allow the user to customize BaseFinder to virtually any t ype of trace processing. We have developed an extensive set of data pr ocessing and analysis modules for use with the program in fluorescence -based sequencing Gellmager is a framework for gel image manipulation. It can be used for gel visualization, lane retracking, and as a front end to the Washington University Getlanes program. The programs were designed using a cross-platform development environment, currently all owing them to run in Windows NT, Windows 95, Openstep/Mach, and Rhapso dy. Work is ongoing to deploy the software on additional platforms, in cluding Solaris, Linux, and MacOS. This software has been thoroughly t ested and debugged in the analysis of >2 million bp of raw sequence da ta from human chromosome 19 region q13. Overall sequencing accuracy wa s measured using a significant subset of these data, consisting of sim ilar to 600 sequences, by comparing the individual shotgun sequences a gainst the final assembled contigs. Also, results are reported from ex periments that analyzed the accuracy of the software and two other wel l-known base-calling programs For sequencing the M13mp18 vector sequen ce.