Table 1 Summary of progressive multiple sequence alignment components
From: Parallel progressive multiple sequence alignment on reconfigurable meshes
Component | input size | processors | run-time |
|---|---|---|---|
2-input max switch | 1 - bit | 1 | 1 broadcast |
4-input max switch | 1 - bit | 4 | 1 broadcast |
2-input max switch | n - bit | n | 1 broadcast |
4-input max switch | n - bit | 4n | 1 broadcast |
on/off switch | n - bit | n ×n +1 | 1 broadcast |
adder/subtractor | n | k ×n, k ≤ n | 1 broadcast |
DP(const. scoring) | 2 sequences, max length = n | O(n3) | 1 broadcast |
DP (general scoring) | 2 sequences, max length = n | O(kn3), k ≤ n | 1 broadcast |
DP back-tracking | n × n | n × n × n | O(1) |
Neighbor-Joining | m × m | O(m3) | O(m) |
Sum-of-pair | 2 pre-aligned groups of m sequences | m × n2 | O(1) |
MSA(const. scoring) | m sequences, max length = n | O(m × n3) | O(m) |
MSA | m sequences, max length = n | O(m × n4) | O(m) |