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Table 1 Comparison of results.

From: Clustering exact matches of pairwise sequence alignments by weighted linear regression

 

No. of contigs

Average contig length

Time in MUMmer

Time using linear regression

Set 1

2

60848

102.003 s

0.922 + 0.037 = 0.959 s

Set 2

3

43489

124.064 s

0.823 + 0.034 = 0.857 s

Set 3

3

41227

108.776 s

0.889 + 0.034 = 0.923 s

Set 4

9

14389

39.470 s

0.881 + 0.047 = 0.928 s

Set 5

44

2621

5.182 s

0.881 + 0.127 = 1.008 s

Set 6

36

2210

2.963 s

0.884 + 0.102 = 0.986 s

Set 7

18

1810

1.772 s

0.861 + 0.053 = 0.914 s

  1. Comparing alignment of several sets of contigs (assembled from a BAC in O. glaberrima) to a reference chromosome (in O. sativa) using only MUMmer and using MUMmer with weighted linear regression. The time using linear regression is shown as the sum between the time MUMmer takes to find the set of seeds plus the execution time of the weighted linear regression algorithm. (See the text for detailed discussion).