tailfindr

tailfindr estimates poly(A) tail lengths from Oxford Nanopore Technologies (ONT) long-read base-called sequencing data to quantify polyadenylation of native RNA and cDNA.

Key Features:

• Direct measurement from long reads: Operates on unaligned, base-called ONT sequencing reads to measure poly(A) tail lengths from native RNA or DNA, including full-length cDNA isoforms with intact poly(A) tails.
• Compatibility with ONT sequencing: Addresses ONT-specific challenges in resolving long homopolymeric stretches by estimating tail lengths that are not reliably reported by base-calling alone.
• Versatility across sequencing conditions: Has been assessed across a range of poly(A) lengths and sequencing conditions, enabling analysis across diverse experimental setups.

Scientific Applications:

• Genome-wide poly(A) length assessment: Enables genome-wide measurement of poly(A) tail length to link genes to polyadenylation profiles without relying on short-read alignment.
• Functional studies of mRNA regulation: Provides precise poly(A) length measurements to study effects on mRNA nuclear export, stability, and translation efficiency.
• Full-length isoform analysis: Permits analysis of full-length cDNA isoforms with intact poly(A) tails to investigate alternative splicing and isoform-specific regulation.

Methodology:

Processes unaligned, base-called ONT sequencing data and applies algorithms specifically designed to detect and measure poly(A) tail lengths, overcoming the challenges of long homopolymeric sequences in nanopore reads.