RaptRanker

RaptRanker ranks candidate RNA aptamer sequences from HT-SELEX data by integrating local nucleotide sequence and secondary structure information to prioritize sequences with high potential binding affinity.

Key Features:

• Integrated Sequence and Structural Analysis: Simultaneously analyzes nucleotide sequences and secondary structures from HT-SELEX datasets to capture sequence and structural motifs relevant to binding.
• Scoring and Ranking Mechanism: Assigns scores to sequences based on local structure and sequence frequency and ranks candidates by these scores to identify high-affinity aptamers.
• Performance Superiority: Demonstrated superior performance relative to Frequency, Enrichment, and MPBind in comparative evaluations and identified essential subsequence motifs validated in two new HT-SELEX experiments.
• Consideration of Secondary Structures: Incorporates secondary structure information into scoring to enhance selection accuracy from complex HT-SELEX datasets.

Scientific Applications:

• Aptamer Selection: Identification and prioritization of RNA aptamers as affinity reagents from HT-SELEX datasets.
• Therapeutic and Diagnostic Development: Selection of candidate RNA aptamers for therapeutic interventions and diagnostic tools.
• Biochemical Research: Discovery of subsequence motifs and structure–function relationships relevant to molecular biology and biochemical studies.

Methodology:

Analyzes HT-SELEX data by integrating sequence frequency with local secondary structure information, assigns scores reflecting potential binding affinity, ranks sequences by those scores, and performs comparative evaluations against Frequency, Enrichment, and MPBind, with validation reported from two new HT-SELEX experiments that confirmed predicted subsequence motifs.