Multiple Sequence Search

A life science portal was enhanced with powerful multi-sequence search functionality, enabling researchers to query multiple nucleotide or peptide sequences simultaneously across comprehensive biological databases.

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All Technologies Used

C
C
C++
C++
NVIDIA CUDA
NVIDIA CUDA

Motivation

The client approached Azati to develop an advanced search tool that could handle multiple sequence queries simultaneously. The goal was to streamline analytical and research workflows by automating the comparison of interrelated biological data points, enabling efficient identification of complex genetic patterns.

Main Challenges

Challenge 1
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.

Challenge 2
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.

Key Features

  • Multi-query input: Supports simultaneous searching with up to six nucleotide or protein sequences, improving research productivity.
  • Advanced document scoring: Ranks documents based on the number of matching sequences and highlights key alignments.
  • Exportable reports: Generates reports in four formats, making results easy to analyze and share within research teams.

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.

Project Impact

Accelerated Research: Enabled scientists to identify complex genetic constructs significantly faster with GPU-powered search.

Increased Precision: Improved result relevance by identifying multiple sequence hits within a single document.

Enhanced Workflow: Simplified data interpretation through visual alignment tools and structured output.

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