3 papers
cs.DS2019
De(con)struction of the lazy-F loop: improving performance of Smith Waterman alignment
Roman Snytsar
Striped variation of the Smith-Waterman algorithm is known as extremely efficient and easily adaptable for the SIMD architectures. However, the potential for improvement has not be…
cs.DS2018
Parallel approach to sliding window sums
Roman Snytsar, Yatish Turakhia
Sliding window sums are widely used in bioinformatics applications, including sequence assembly, k-mer generation, hashing and compression. New vector algorithms which utilize the…
cs.DS2018
Vectorized Character Counting for Faster Pattern Matching
Roman Snytsar
Many modern sequence alignment tools implement fast string matching using the space efficient data structure called FM-index. The succinct nature of this data structure presents un…