Comma-free code alignment for single-cell microbial detection

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Solution Overview

Problem

Existing methods for detecting viruses in sequencing data rely on reference genomes and lack single-cell resolution, making it difficult to identify novel microbes effectively.

Innovation Solution

The method involves converting reference sequences and sample sequences into comma-free codes, aligning these codes to generate a microbe profile, and detecting the presence of microbes in a sample while retaining single-cell resolution.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If reference genome-based methods are used for viral detection, then detection accuracy is improved, but single-cell resolution is lost

Engineering Contradiction:

Improvedetection accuracyVSAvoidsingle-cell resolution

Core Design Contradiction:

Measurement precisionVSQuantity of substance

Solution Approach 1:

The patent segments the sequencing data at the single-cell level, processing and analyzing reads from individual cells separately while maintaining reference genome-based detection accuracy. This allows simultaneous achievement of both high detection accuracy through reference matching and single-cell resolution through individual cell data processing.

Inventive Principle:

Principle #1Segmentation

2Reliability

If reference genome-based methods are used, then detection reliability is improved, but ability to detect novel microbes is reduced

Engineering Contradiction:

Improvedetection reliabilityVSAvoiddetection of novel microbes

Core Design Contradiction:

ReliabilityVSAdaptability or versatility

Solution Approach 1:

The patent performs preliminary actions by pre-processing sequencing data at the single-cell level and preparing reference databases before actual detection. This preliminary preparation enables the system to reliably detect known pathogens while also capturing signals from novel microbes through sophisticated alignment algorithms that can identify patterns even without exact reference matches.

Inventive Principle:

Principle #10Preliminary action

3Productivity

If traditional alignment methods are used, then computational efficiency is improved, but detection sensitivity for novel viruses is reduced

Engineering Contradiction:

Improvecomputational efficiencyVSAvoiddetection sensitivity

Core Design Contradiction:

ProductivityVSMeasurement precision

Solution Approach 1:

The patent creates a simplified representation or copy of the reference genome structure that enables fast computational alignment while maintaining the sensitivity to detect novel viruses. This copied reference structure allows rapid processing of single-cell data without sacrificing detection sensitivity for previously unknown viral pathogens.

Inventive Principle:

Principle #26Copying

Data Source

PatentUS20250191691A1Methods for the translated alignment of transcriptomic data at single-cell resolution

Publication Date: 2025.06.12 CALIFORNIA INST OF TECH

AI summary

Disclosed herein include method and systems suitable for use in detection and/or prediction of microorganisms in a sample using sequencing data. In some embodiments, the method comprises converting reference sequences and sample sequences to comma-free sample codes; and detecting the presence of microbes in the sample based on alignment of the comma-free codes. In some embodiments, the method comprises detecting and/or predicting viral presence in host cell, by identifying and analyzing signature host genes. In some embodiments, the system suitable for performing the methods disclosed herein.