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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, kn 1 broadcast
DP(const. scoring) 2 sequences, max length = n O(n3) 1 broadcast
DP (general scoring) 2 sequences, max length = n O(kn3), kn 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)
  1. This Table summarizes all the parallel components developed in this study along with their time and CPU complexity.