Accelerated Research
Enabled researchers to perform multi-sequence queries significantly faster, reducing project timelines and increasing the speed of genetic discovery.
Technologies used
C
C++
NVIDIA CUDA
Motivation
The client approached Azati to reduce the time and effort required for multi-sequence analysis, improve the accuracy and relevance of search results, and automate the comparison of multiple nucleotide or protein sequences across large biological databases. The goal was to streamline research workflows, minimize manual errors, and enable scientists to efficiently identify complex genetic patterns and alignments.
Main challenges
Challenge 01
Enabling Multi-Sequence Search for Genetic Engineering
Biological scientists needed a tool to search for multiple nucleotide or protein sequences at once, which was critical for identifying CDRs, chimeric constructs, and recombinant plasmids. At the time, no such tool existed in the market. Azati proposed the design and development of a new multiple sequence search feature from scratch.
#1
Challenge 02
No Multi-Sequence Patent Analysis
Researchers lacked the ability to correlate multiple sequences across various claims within the same patent document, limiting the accuracy and depth of results. Azati addressed this by building an advanced scoring system and enhanced interface to ensure precise multi-alignment tracking.
#2
Our approach
Domain Needs Analysis
Analyzed the client’s domain-specific needs for multi-sequence comparisons and patent research workflows.
MSS Engine Development
Designed and developed the Multiple Sequence Search (MSS) engine capable of processing up to six sequence inputs simultaneously.
High-Performance Alignment
Implemented enhanced Smith-Waterman algorithm for high-performance, GPU-accelerated matching with 30–50x speed improvement.
Scoring and Ranking System
Created a scoring and ranking system to prioritize documents with multiple matching sequences.
User Interface and Reporting
Developed a user-friendly interface with support for combined alignment view and four exportable report formats.
Seamless Integration
Integrated the tool into the client’s existing bioinformatics portal, ensuring seamless access and compatibility.
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01
Multi-Query Input
Supports simultaneous input of up to six nucleotide or protein sequences, allowing researchers to run complex queries efficiently. This improves productivity by reducing the time needed for sequential searches and enables simultaneous comparison of related genetic sequences.
Key capabilities:
- Input multiple nucleotide or peptide sequences at once
- Perform simultaneous searches across multiple biological databases
- Streamline research workflows with batch query support
- Reduce repetitive manual searches
02
Advanced Document Scoring
Ranks search results based on the number of matching sequences and key alignments. Documents containing multiple hits are prioritized, ensuring that researchers focus on the most relevant results. The scoring system enhances accuracy and relevance for complex genetic research.
Key capabilities:
- Prioritize documents with the highest number of matching sequences
- Highlight key alignment regions for easy identification
- Ensure relevance of search results through advanced scoring
- Support identification of overlapping or related sequences in patents
03
GPU-Accelerated Alignment
Implements an optimized Smith-Waterman algorithm with NVIDIA CUDA GPU acceleration, achieving up to 50x faster sequence alignment without compromising accuracy. Enables high-performance processing of large sequence datasets for rapid genetic research.
Key capabilities:
- Leverage GPU processing for high-speed alignment
- Maintain high accuracy in sequence comparisons
- Handle large datasets efficiently
- Accelerate research workflows by reducing computational time
04
Multi-Sequence Patent Analysis
Allows correlation of multiple sequences within single or multiple patent documents. Researchers can detect overlapping claims and track complex genetic constructs across patents, improving intellectual property analysis and scientific discovery.
Key capabilities:
- Search for multiple sequences within the same patent document
- Identify sequences present in different claims
- Support advanced IP and research analysis
- Visualize sequence overlaps for easier interpretation
05
Exportable Reports
Generates search results in four different report formats with detailed alignment views. Reports can be shared with collaborators or integrated into laboratory workflows, supporting reproducibility and collaboration.
Key capabilities:
- Export results in multiple file formats
- Include visual sequence alignments in reports
- Enable easy sharing with research teams
- Integrate results into downstream bioinformatics pipelines
06
User-Friendly Interface
Provides an intuitive interface for visualizing multi-sequence alignments and tracking search progress. Researchers can quickly interpret results, toggle between combined or individual sequence views, and navigate efficiently between datasets.
Key capabilities:
- Visualize sequence alignments clearly
- Switch between individual and combined alignment views
- Navigate large datasets efficiently
- Simplify interpretation of complex multi-sequence search results
Results & business impact
Increased Accuracy
Advanced scoring and GPU-accelerated alignments improved precision in identifying relevant genetic sequences and patent claims.
Enhanced Workflow
Exportable reports and a user-friendly interface simplified data interpretation and collaboration, streamlining daily research activities.
Improved Patent Analysis
Multi-sequence patent correlation allowed scientists to identify overlapping sequences and track complex genetic constructs across claims, improving IP research and compliance.
Time and Resource Efficiency
High-performance GPU processing reduced computational overhead, allowing teams to focus on analysis rather than waiting for results.
