|
Counts for selected HCNE sets |
|||||
| Criteria for HCNE detection |
Number of HCNEs detected in indicated comparison |
||||
|
|
|
||||
| Minimum identity |
Minimum size (bp) |
Human vs mouse |
Human vs chicken |
Human vs zebrafish |
Zebrafish vs Tetraodon |
|
|
|||||
| 80% over 30 columns |
30 |
NC |
125,174 |
19,596 |
57,681 |
| 90% over 30 columns |
30 |
NC |
78,831 |
8,260 |
26,157 |
| 96% over 30 columns |
30 |
305,015 |
50,478 |
3,656 |
10,205 |
| 100% |
30 |
150,487 |
35,338 |
1,721 |
4,737 |
| 70% over 50 columns |
50 |
NC |
93,162 |
16,725 |
45,828 |
| 80% over 50 columns |
50 |
NC |
63,304 |
7,169 |
25,997 |
| 90% over 50 columns |
50 |
265,537 |
36,794 |
3,127 |
8,610 |
| 95% over 50 columns |
50 |
107,860 |
22,530 |
1,228 |
3,078 |
| 98% over 50 columns |
50 |
68,600 |
17,579 |
763 |
1,782 |
| 100% |
50 |
34,785 |
11,934 |
330 |
754 |
| 90% over 50 columns |
100 |
81,065 |
15,339 |
733 |
1,695 |
| 95% over 50 columns |
100 |
25,801 |
7,901 |
188 |
450 |
| 100% |
100 |
4,919 |
2,475 |
20 |
61 |
| 100% |
200 |
494 |
365 |
0 |
2 |
|
Counts indicate the number of HCNEs obtained by collapsing HCNEs onto the assembled chromosomes of selected reference genomes. HCNEs were counted in this way to reduce redundancy and thereby make counts more comparable between data sets. The underlying Ancora data sets are not biased by selecting either genome as a reference. Note that HCNEs are generally larger than the window size (30 or 50) used to identify them because the procedure that detects HCNEs merges overlapping conserved elements. NC, not calculated. | |||||
Engström et al. Genome Biology 2008 9:R34 doi:10.1186/gb-2008-9-2-r34 |
|||||