Figure 1

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[8]. (B) Vectors along the query, described by Rognes and Seeberg [9]. (C) Striped approach, described by Farrar [10]. (D) Multi-sequence vectors, described by Alpern et al[6]. and in this paper.