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Table 1 Results on analytical criteria investigated in a comparative study on PRRSV sequence alignment algorithmsa

From: Impact of alignment algorithm on the estimation of pairwise genetic similarity of porcine reproductive and respiratory syndrome virus (PRRSV)

Criterion Algorithm
Clustal W MAFFT T-Coffee Muscle Clustal 0mega 
1. Similarity: average pairwise genetic similarity (%) of aligned sequences within the dataset (mean ± standard deviation)
 Replicate 1 (1191 sequences) 88.77 ± 4.19 88.84 ± 4.17 88.71 ± 4.23 88.78 ± 4.19 88.78 ± 4.19
 Replicate 2 (1191 sequences) 88.68 ± 4.11 88.69 ± 4.11 88.28 ± 4.31 88.69 ± 4.11 88.69 ± 4.11
2. Proportion of pairwise comparisons of sequences having ≥ 97.5% genetic similarity (%)
 Replicate 1 (1191 sequences) 5.17 5.17 5.19 5.17 5.17
 Replicate 2 (1191 sequences) 4.91 4.91 4.66 4.91 4.91
3. Length of aligned dataset: number of sites per sequence in the aligned dataset
 Replicate 1 (1191 sequences) 603 606 607 603 603
 Replicate 2 (1191 sequences) 603 603 609 603 603
4. Average sum of pairs (SP) score: proportion of shared homologies with reference alignment (%)b
 Clustal W as reference 99.93 99.74 99.91 99.94
 MAFFT as reference 99.93 99.78 99.97 99.97
 T-Coffee as reference 99.92 99.96 99.94 99.97
 Muscle as reference 99.91 99.97 99.76 99.95
 Clustal Omega as reference 99.94 99.97 99.78 99.95
Average 99.92 99.95 99.76 99.94 99.95
5. Congruent cells ≥ 97.5% similarity: proportion of cells between two pairwise similarity matrices having the same binary value (0: < 97.5%; 1: ≥97.5%) for genetic similarityb
 Clustal W as reference 100.00 99.86 99.99 99.99
 MAFFT as reference 100.00 99.86 99.99 99.99
 T-Coffee as reference 99.86 99.86 99.86 99.86
 Muscle as reference 99.99 99.99 99.86 99.99
 Clustal Omega as reference 99.99 99.99 99.86 99.99
Average 99.96 99.96 99.86 99.95 99.95
  1. aThe open gap penalties used was 30 for Clustal W, 7 for MAFFT, −200 for T-Coffee, −1000 for Muscle and default for Clustal Omega. The dataset included 2383 sequences collected in 2010–2014 divided in two replicates
  2. bAverage of 2 replicates of 1191 sequences