UTILIZATION OF SPECIALIZED HARDWARE FOR DNA SEQUENCE ANALYSIS

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An ABI inherit system was purchased by DCRT and is being made available as a shared resource to NIH intramural scientists. Scientists purchase Macintosh client software from ABI and access the Inherit system over the NIH network. Inherit makes heavy use of specialized hardware, the Fast Data Finder (FDF), a parallel processor capable of scanning and comparing over 15 million characters per second. This system is primarily designed for: (1) assembly of medium to large sequencing projects; (2) searching the gene and protein databases for homologous gene sequences; and (3) searching quickly for genetic motifs such as regulatory elements. A pattern search language incorporated in the system allows for very complicated query formulations. DCRT is pursuing discussions with ABI on a cooperative agreement to allow DCRT access to source code to port Server software to additional UNIX platforms, including the NIH Convex. In connection with the ABI Inherit evaluation, a critical, quantitative comparison was done of several different commercial computer programs designed for sequence assembly and analysis. The purpose of this study was two fold: (1) to gain experience and expertise in the use of several different sequence assembly programs; and (2) to evaluate these programs as to their speed and accuracy in assembly and in their ease of use. Six sequence assembly packages have been examined. To evaluate the speed and quality of sequence assembly, the rat multidrug resistant gene (RATMDRM, 5,254 base pairs) sequence was randomly split into 58 overlapping fragments, each 200-400 basepairs in length. From 0 to 15% error was randomly added to these fragments based on the distribution of error found in the original fragments that were used to find the assembly.