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Bioinformatics Algorithm Enhancement: BLAST Optimization

Azati optimized the BLAST algorithm to improve accuracy when working with short DNA/RNA sequences, enabling a biotechnology company to conduct more reliable primer-based research and improve the effectiveness of their genomic sequence analysis.

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All Technologies Used

C
C
C++
C++

Motivation

The client approached Azati with a request to improve the performance of the BLAST algorithm for short sequence searches. The goal was to eliminate inaccuracies caused by default parameters and ensure that even sequences shorter than 20 bases yield meaningful and complete results.

Main Challenges

Challenge 1
BLAST's Short-Primer Problem

Researchers working with short primer sequences were not getting sufficient matches from the BLAST algorithm, as it missed significant alignments due to strict default parameters. Azati proposed customizing the algorithm to adjust its sensitivity and thresholds, ensuring better results for short queries.

Challenge 2
BLAST's Short-Sequence Bias

The default configuration of BLAST prioritized longer sequences, which severely limited its effectiveness for specialized short-sequence research. Azati addressed this by redesigning the system to support dynamic parameter tuning based on input length.

Key Features

  • Short-sequence optimization: Enhanced algorithm accuracy for queries under 20 bases, critical for primer-based analysis.
  • Dynamic parameter control: System automatically adjusts settings based on query characteristics, removing manual configuration burden.
  • Custom filters: Additional filters boost precision and relevance of search outcomes for niche biological queries.

Our Approach

Use Case and Limitation Analysis
Analyzed the client’s use case focused on primer matching and identified the limitations of the default BLAST settings for short sequences.
Algorithm Parameter Customization
Customized BLAST algorithm parameters, lowering the significance threshold and adjusting sequence length filters to increase sensitivity for queries under 20 bases.
Dynamic Adjustment Implementation
Implemented dynamic system behavior to auto-adjust these values on the search page, ensuring consistent performance without requiring user intervention.
Enhanced Filtering Logic
Integrated additional filters into the algorithm logic to refine search accuracy and reduce false negatives.
Core Codebase Optimization
Modified the core BLAST codebase to embed the optimizations into the system, making it scalable and robust for long-term research use.

Project Impact

Improved Accuracy: Researchers gained access to significantly more relevant matches, even for very short sequences.

Increased Productivity: Eliminated the need for manual reconfiguration, enabling faster, more intuitive search operations.

Research Advancement: Empowered the client to conduct higher quality genetic studies, especially in therapeutic discovery and personalized medicine.

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