System to compare at least one dna fragment to a reference genome

Abstract

A computer system and method for sequencing deoxyribonucleic acid (DNA), to determine the order of the different nucleotides in a genomic sequence or sequence fragment. An alignment system employs a direct 'brute force' Hamming distance calculation between a read sequence and a reference genome. The alignment system is configured to compare directly a set of DNA fragments to a reference genome in a short period, and with the higher probability of accuracy than similar comparison systems given the same number of clock cycles. Each DNA fragment is compared with a reference genome for the entire length of the latter using arrangements of memory cells for storing read sequences and inverse complements of the read sequences, shift registers for streaming the reference genome, and circuitry for calculating and summing the distance between the reference, the read sequence, and the inverse complement in parallel. Both digital and analog implementations are described.