SigAlign

SigAlign employs two explicit cutoffs for sequence alignment results—minimum length and maximum penalty per length—alongside three affine gap penalties to provide a transparent, non-heuristic alignment process for read mapping and database searches.

Key Features:

• Explicit similarity cutoffs: Uses minimum length and maximum penalty per length as explicit criteria for alignment results.
• Affine gap penalties: Incorporates three affine gap penalties into the alignment scoring system.
• Non-heuristic approach: Provides high sensitivity without relying on approximation techniques used by heuristic aligners.
• High throughput: Surpasses the throughput of existing heuristic aligners, particularly for high-accuracy reads or genomes with few repetitive regions.
• Open-source library: Offers a customizable alignment process suitable for integration into new analytical algorithms, tools and pipelines.

Scientific Applications:

• Read mapping: Maps sequencing reads to reference genomes with high sensitivity and throughput.
• Database searches: Performs sequence similarity searches against biological databases with explicit, transparent output criteria.

Methodology:

SigAlign uses a gap-affine sequence alignment algorithm guided by explicit similarity cutoffs.