Block aligner: fast and flexible pairwise sequence alignment with SIMD-accelerated adaptive blocks

Background The Smith-Waterman-Gotoh alignment algorithm is the most popular method for comparing biological sequences. Recently, Single Instruction Multiple Data methods have been used to speed up alignment. However, these algorithms have limitations like being optimized for specific scoring schemes, cannot handle large gaps, or require quadratic time computation. Results We propose a new algorithm called block aligner for aligning nucleotide and protein sequences. It greedily shifts and grows a block of computed scores to span large gaps within the aligned sequences. This greedy approach is able to only compute a fraction of the DP matrix. In exchange for these features, there is no guarantee that the computed scores are accurate compared to full DP. However, in our experiments, we show that block aligner performs accurately on various realistic datasets, and it is up to 9 times faster than the popular Farrar’s algorithm for protein global alignments. Conclusions Our algorithm has applications in computing global alignments and X -drop alignments on proteins and long reads. It is available as a Rust library at . ### Competing Interest Statement The authors have declared no competing interest. * AVX : Advanced Vector Extensions DP : Dynamic Programming SIMD : Single Instruction Multiple Data