Serial Nucleotide Comparison Circuit with Enveloping Thresholds

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Solution Overview

Problem

Existing customized integrated circuits for Smith Waterman analysis, such as FPGAs, face inefficiencies due to the need for parallel processing, which consumes significant spatial fabric and prevents optimization in specific instances, especially when performing nucleotide sequence alignment.

Innovation Solution

Implementing a series-based Smith Waterman analysis using customized integrated circuitry that leverages enveloping thresholds to demarcate necessary and unnecessary nucleotide comparisons, allowing for a single calculation engine to generate scores for individual cells of a two-dimensional matrix, and utilizing multiple control units to optimize processing speed and frequency.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Speed

If parallel processing is used for Smith Waterman analysis in customized integrated circuits, then processing speed is improved, but spatial fabric consumption increases significantly

Engineering Contradiction:

Improveprocessing speedVSAvoidspatial fabric

Core Design Contradiction:

SpeedVSArea of stationary object

Solution Approach 1:

The patent divides the Smith Waterman matrix into multiple smaller matrices, each processed by a dedicated control unit and calculation engine. This segmentation allows parallel processing of multiple sequence alignment tasks simultaneously while reducing the spatial footprint required for each individual processing unit, thereby resolving the contradiction between processing speed and spatial fabric consumption.

Inventive Principle:

Principle #1Segmentation

Solution Approach 2:

The patent transitions from traditional two-dimensional parallel processing to a multi-dimensional approach by introducing multiple control units and calculation engines operating in parallel across different spatial and temporal dimensions. This enables efficient use of limited spatial fabric while maintaining high processing throughput through coordinated multi-unit operation.

Inventive Principle:

Principle #17Another dimension (Dimensionality change)

2Speed

If parallel processing is implemented for Smith Waterman analysis, then processing speed is improved, but optimization in specific instances is prevented

Engineering Contradiction:

Improveprocessing speedVSAvoidoptimization capability

Core Design Contradiction:

SpeedVSAdaptability or versatility

Solution Approach 1:

The patent implements dynamic control units that can adaptively adjust processing parameters and select optimal calculation paths based on the specific characteristics of input nucleotide sequences. This dynamic adaptability allows the system to optimize performance for specific instances while maintaining parallel processing capabilities across multiple tasks, resolving the contradiction between fixed parallel processing and instance-specific optimization.

Inventive Principle:

Principle #15Dynamics

Solution Approach 2:

Each control unit and calculation engine is designed with specialized functionality tailored to specific regions or types of sequence alignment tasks. This local quality approach enables each processing unit to be optimized for its specific function while the overall system maintains parallel processing capability, allowing simultaneous optimization for different instances.

Inventive Principle:

Principle #3Local quality

3Productivity

If multiple control units with single calculation engine are used, then processing frequency is optimized, but physical distance between control units and calculation engine increases

Engineering Contradiction:

Improveprocessing frequencyVSAvoidphysical distance

Core Design Contradiction:

ProductivityVSLength of stationary object

Solution Approach 1:

The patent employs a hierarchical nested architecture where multiple control units are integrated within or adjacent to the calculation engine, with control units nested around shared memory and processing resources. This nested arrangement minimizes physical distance between control units and calculation engine while enabling multiple control units to operate independently, thereby maintaining high processing frequency without significant distance penalties.

Inventive Principle:

Principle #7Nested doll (Nesting)

Data Source

PatentUS10566076B2Customized integrated circuit for serial comparison of nucleotide sequences

Publication Date: 2020.02.18 MICROSOFT TECHNOLOGY LICENSING LLC

AI summary

Comparisons between two nucleotide sequences can be performed by customized integrated circuitry that can implement a Smith Waterman analysis in series, as opposed to the parallel implementations known in the art. Series performance enables such customized integrated circuitry to take advantage of optimizations, including enveloping thresholds that demarcate between cells of a two-dimensional matrix for which nucleotide comparisons are to be performed, and cells of the two-dimensional matrix for which no such comparison need be performed, and, instead, a value of zero can simply be entered. Additionally, such customized integrated circuitry facilitates the combination of multiple control units, each directing the comparison of a unique pair of nucleotides, with a single calculation engine that can generate values for individual cells of the two-dimensional matrices by which such pairs of nucleotides are compared.