|
Comparison of results. |
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| 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 |
|
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). | ||||
González and Liao BMC Bioinformatics 2008 9:102 doi:10.1186/1471-2105-9-102 |
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