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Table 1 Comparison of supported maximum query sequence length

From: CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units

Smith-Waterman Software Maximum Sequence Length
NCBI-BLAST [5] Unlimited
SWPS3 [10] 10K
CBESW [12] 852
SW-CUDA [14] 2050
CUDASW++ 59K