![]() Intermediate results were obtained with five other programs (Sequencher, AssemblyLIGN, XBAP, SeqMan, and AutoAssembler in a mode that made use of an external special processor). Three (GCG, FAB, and AutoAssembler) consistently produced consensus sequences of low error and high reproducibility. The programs could be roughly divided into three groups based on the accuracy and reproducibility of assembly. Similar results were also obtained using other, unrelated sequences. Tests were also done to determine if the order in which fragments were added to a project affected the final sequence and if the quality of assemblage was sequence dependent. The quality of the assemblages was evaluated by comparing the number of differences between the assembled sequence and the original sequence. From 0 to 15% error was then added to independent sets of fragments, and assemblage was attempted. ![]() The probability of an error, and the type of error, was modified using an error distribution template that was developed by comparing the original fragments used to sequence RATMDRM with the final, edited sequence stored in GenBank. Various degrees of error, in the form of miss-identified bases, missed bases, and duplicated bases, were randomly added to these fragments. To test the assemblers under controlled conditions, the rat multidrug resistance (RATMDRM) gene sequence was randomly divided into overlapping 200- to 400-base fragments. We have compared 11 sequence assembly programs for the accuracy and reproducibility with which they assemble DNA fragments into a completed sequence.
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