Table 1

Summary of progressive multiple sequence alignment components

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)


This Table summarizes all the parallel components developed in this study along with their time and CPU complexity.

Nguyen et al. BMC Genomics 2011 12(Suppl 5):S4   doi:10.1186/1471-2164-12-S5-S4

Open Data