# Frameshift-aware sequence alignment

Long-read DNA often carries frameshift errors, and aligning it to protein family profiles has meant either translating six reading frames or correcting errors first, both of which cost sensitivity. DUMMEST follows DUMMER's length-bias-free alignment idea and adds nucleotide-emitting indel states to the match, insert and delete states, approximating frameshifts with combinations of nucleotides and codons, with GPU-accelerated MMseqs2 multistage prefiltering. On simulated long reads it detects more alignments with greater average length, matches BATH in sensitivity, improves specificity under simulated sequencing artifacts, and runs 2–12× faster depending on dataset.

Long-read DNA often carries frameshift errors, and aligning it to protein family profiles has meant either translating six reading frames or correcting errors first, both of which cost sensitivity. DUMMEST follows DUMMER's length-bias-free alignment idea and adds nucleotide-emitting indel states to the match, insert and delete states, approximating frameshifts with combinations of nucleotides and codons, with GPU-accelerated MMseqs2 multistage prefiltering. On simulated long reads it detects more alignments with greater average length, matches BATH in sensitivity, improves specificity under simulated sequencing artifacts, and runs 2–12× faster depending on dataset.