  Dot plots are a standard method for local comparison of biological sequences.
In a dot plot, a substring to substring distance is computed for all pairs of
fixed-size windows in the input strings. Commonly, the Hamming distance is used
since it can be computed in linear time. However, the Hamming distance is a
rather crude measure of string similarity, and using an alignment-based edit
distance can greatly improve the sensitivity of the dot plot method. In this
paper, we show how to compute alignment plots of the latter type efficiently.
Given two strings of length m and n and a window size w, this problem consists
in computing the edit distance between all pairs of substrings of length w, one
from each input string. The problem can be solved by repeated application of
the standard dynamic programming algorithm in time O(mnw^2). This paper gives
an improved data-parallel algorithm, running in time $O(mnw/\gamma/p)$ using
vector operations that work on $\gamma$ values in parallel and $p$ processors.
We show experimental results from an implementation of this algorithm, which
uses Intel's MMX/SSE instructions for vector parallelism and MPI for
coarse-grained parallelism.
