ASSIGNMENT OF POSITION-SPECIFIC ERROR-PROBABILITY TO PRIMARY DNA-SEQUENCE DATA

DNA sequence predicted from polyacrylamide gel-based technologies is i naccurate because of variations in the quality of the primary data due to limitations of the technology, and to sequence-specific variations due to nucleotide interactions within the DNA molecule and with the g el. The ability to recognize the probability of error in the primary d ata will be useful in reconstructing the target sequence of a DNA sequ encing project, and in estimating the accuracy of the final sequence. This paper describes the use of linear discriminant analysis to assign position-specific probabilities of incorrect, over- and under- predic tion of nucleotides for each predicted nucleotide position in primary sequence data generated by a gel-based DNA sequencing technology. Usin g this method, most of the error potential in primary sequence data ca n be assigned to a limited number of discrete positions. The use of pr obability values in the sequence reconstruction process, and in estima ting the accuracy of consensus sequence determination is described.