In2h2

Mickey Lee Fandrich

Vardan Movsisyan

Bruce Kent McCormick

Christopher John McCormick

Matthew McCormick

William Harry Nagel

Ludovico Minati

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.

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

A nonlinear neuron classifier comprising a neuron array including a plurality of neuron chips each including a plurality of neurons of variable length and variable depth, the chips processing input vectors of variable length and variable depth that are input into the classifier for comparison against vectors stored in the classifier, wherein an NSP flag is set for a plurality of the neurons to indicate that only that plurality of neurons is to participate in the vector calculations. A virtual content addressable memory flag is set for certain of the neuron chips to enable functions including fast readout of data from the chips. Results of vector calculations are aggregated for fast readout for a host computer interfacing with the classifier.

Hardware enhancements to radial basis function with restricted coulomb energy learning and/or k-Nearest Neighbor based neural network classifiers

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Oregon City, OR, United States of America

Mickey Lee Fandrich