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.