Treffer: Processing repetitive sequence structures with mismatches at streaming rate

With the accelerating growth of biological databases and the beginning of genome-scale processing, cost-effective high-performance sequence analysis remains an essential problem in bioinformatics. We examine the use of FPGAs for finding repetitive structures such as tandem repeats and palindromes under various mismatch models. For all problems addressed here, we process strings in streaming mode and obtain processing times of 5ns per character for arbitrary length strings. Using a Xilinx XC2VP100, we can find: (i) all repeats up to size 1024, each with any number of mismatches; (ii) all precise tandem arrays with repeats up to size 1024; (iii) all palindromes up to size 256, each with any number of mismatches, or (iv) a somewhat smaller size of (i) and (iii) with a single insertion or deletion. The speed-up factors range from 250 to 6000 over an efficient serial implementation which is itself many times faster than a direct implementation of a theoretically optimal serial algorithm.