Approaches to vectorisation of Smith-Waterman alignments. Alignment matrices are shown with the elements that form the first five vectors processed indicated in black, blue, red, green and yellow. For simplicity, vectors of only 4 elements are shown, while 16 elements would normally be used. (A) Vectors along the anti-diagonal, described by Wozniak et al. (B) Vectors along the query, described by Rognes and Seeberg . (C) Striped approach, described by Farrar . (D) Multi-sequence vectors, described by Alpern et al. and in this paper.
Rognes BMC Bioinformatics 2011 12:221 doi:10.1186/1471-2105-12-221