Publication details

Hardware Acceleration of Approximate Tandem Repeat Detection

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Year of publication 2010
Type Article in Proceedings
Conference 18th IEEE Symposium on Field-Programmable Custom Computing Machines
MU Faculty or unit

Faculty of Informatics

Field Computer hardware and software
Keywords Approximate tandem repeat; dynamic programming; systolic array; FPGA; DNA;
Description Understanding the structure and function of DNA sequences represents an important area of research in modern biology. Unfortunately, analysis of such data is often complicated by the presence of mutations introduced by evolutionary processes.They increase the time-complexity of algorithms for sequence analysis by introducing an element of uncertainty, complicating their practical usage. This paper investigates the possibilities for hardware acceleration of approximate tandem repeat searching and describes a parametrized architecture suitable for chips with FPGA technology. The proposed architecture is able to detect tandems with both types of errors (mismatches and indels) and does not limit the length of detected tandem. A prototype of the circuit was implemented in VHDL language and synthesized for Virtex5 technology. Application on test sequences shows that the circuit is able to speed up tandem searching in orders of thousands in comparison with the best-known software method relying on suffix arrays.
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