• Korean Journal of Microbiology
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• v.34 no.1_2
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• pp.58-63
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• 1998

Fragment assembly problem is to reconstruct DNA sequence contigs from a collection of fragment sequences. We have developed an efficient X-window program, XFAP, for assembling DNA fragments. In the XFAP, the dimer frequency comparison method is used to quickly eliminate pairs of fragments that can not overlap. This method takes advantage of the difference of dimer frequencies within the minimum acceptable overlap length in each fragment pair. Hirschberg algorithm is applied to compute the maximal-scoring overlapping alignment in linear space. The perfomance of XFAP was tested on a set of DNA fragment sequences extracted from long DNA sequences of GenBank by a fragmentation program and showed a great improvement in execution time, especially as the number of fragments increases.