FSBC

FSBC performs fast string-based clustering of HT-SELEX oligonucleotide sequences to identify over-represented strings of varying lengths as potential aptamer target binding regions.

Key Features:

• Single-round cluster estimation: Performs cluster estimation from a single (typically final) round of HT-SELEX data to identify sequence groups that include potential aptamers.
• Over-represented string detection: Focuses on identifying over-represented strings as candidate target binding regions to reduce the search space.
• Variable-length motif search: Searches for over-represented strings across multiple lengths to account for variability in target binding region length.
• Robustness to nucleobase imbalance: Accommodates imbalanced nucleobase composition that often results from the aptamer selection process.
• String-based clustering approach: Contrasts with conventional methods that rely on full-length sequence similarity or limited motif lengths by using string-focused clustering.
• Large-scale performance: On HT-SELEX datasets exceeding 15 million oligonucleotide sequences, achieved the highest clustering accuracy and ranked second in calculation speed compared with FASTAptamer, AptaCluster, APTANI, and AptaTRACE.

Scientific Applications:

• Aptamer candidate identification from HT-SELEX: Identifies sequence groups containing potential aptamers from HT-SELEX experiments.
• Large-scale HT-SELEX analysis: Enables clustering and candidate selection on large HT-SELEX datasets, including analyses involving over 15 million oligonucleotides.
• Detection of variable binding regions: Facilitates discovery of target binding regions with variable lengths across different molecules or binding styles.
• Mitigation of selection bias effects: Addresses biases such as imbalanced nucleobase composition introduced during the selection process.

Methodology:

FSBC searches HT-SELEX sequences for over-represented strings across multiple lengths, reduces the search space by using those strings as candidate binding regions, and performs cluster estimation from a single (typically final) round of HT-SELEX data; comparative evaluation was performed against FASTAptamer, AptaCluster, APTANI, and AptaTRACE on datasets exceeding 15 million oligonucleotides.