Detect poly tail type for a single sequence using Dorado-style algorithm

This function implements the Dorado-style poly tail detection algorithm for a single cDNA sequence. It uses edit distance matching of SSP and VNP primer sequences at both ends of the read to determine orientation, testing both forward (polyA) and reverse (polyT) strand configurations.

Usage

detect_orientation_single(sequence)

Arguments

sequence

Character string containing the DNA sequence to classify

Value

Character string: "A" for polyA orientation, "T" for polyT orientation, or "unknown" for unclassified sequences

Examples

if (FALSE) { # \dontrun{
detect_orientation_single("TTTCTGTTGGTGCTGATATTGCTTT...")  # Returns "A"
detect_orientation_single("ACTTGCCTGTCGCTCTATCTTCAG...")   # Returns "T"
} # }