AptaCluster

AptaCluster clusters HT-SELEX aptamer sequence pools to identify sequence families and characterize selection dynamics from deep sequencing across SELEX selection rounds.

Key Features:

• Efficient clustering: Clusters entire HT-SELEX aptamer pools to handle the large volume of sequences produced by deep sequencing.
• Round-aware analysis: Compares and groups sequences across multiple SELEX selection rounds to reveal relationships among sequences over the selection process.
• High-performance implementation: Uses a very fast multiprocessor implementation to accelerate processing of large-scale HT-SELEX datasets.
• SELEX optimization support: Enables analysis that can inform optimization of SELEX experimental design and selection strategies.

Scientific Applications:

• HT-SELEX data analysis: Identifies sequence families and tracks their dynamics across selection rounds in high-throughput SELEX experiments.
• IL-10RA case study: Was applied to datasets targeting the Interleukin 10 receptor alpha chain (IL-10RA) to survey relationships between sequences across selection rounds.

Methodology:

Clustering of entire HT-SELEX aptamer pools with a very fast multiprocessor implementation to analyze sequence relationships across selection rounds.