Table 1.
Sensitivity comparison of indexing algorithms
| Budget | w = 10 | w = 11 | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Fugu | Mouse HHAs | Pig HHAs | Fugu | Mouse HHAs | Pig HHAs | |||||||||||
| HHAs | Exons | HHAs | Exons | |||||||||||||
| S | T | S | T | S | T | S | T | S | T | S | T | S | T | S | T | |
| 1 | 56 | 68 | 57 | 74 | 2020 | 2137 | 6006 | 5998 | 48 | 64 | 46 | 69 | 1856 | 2060 | 5930 | 5949 |
| 1.5 | – | 69 | – | 75 | – | 2240 | – | 6049 | – | 65 | – | 71 | – | 2158 | – | 6027 |
| 2 | 61 | 69 | 65 | 76 | 2190 | 2259 | 6074 | 6079 | 51 | 65 | 52 | 72 | 2089 | 2208 | 6044 | 6034 |
| 3 | 66 | 69 | 70 | 77 | 2258 | 2295 | 6089 | 6086 | 56 | 67 | 61 | 74 | 2186 | 2248 | 6067 | 6079 |
| 5 | 68 | 69 | 72 | 77 | 2302 | 2325 | 6104 | 6096 | 61 | 67 | 67 | 75 | 2256 | 2286 | 6083 | 6084 |
| 7 | 68 | 69 | 75 | 77 | 2324 | 2339 | 6121 | 6098 | 63 | 67 | 70 | 75 | 2283 | 2312 | 6105 | 6089 |
| 10 | 69 | 69 | 76 | 77 | 2338 | 2346 | 6135 | 6115 | 66 | 67 | 74 | 75 | 2301 | 2320 | 6118 | 6092 |
Shown here are sensitivity results for mouse, fugu and pig using an alignment of baboon, cat, chicken, chimp, cow, dog, human, mouse, pig and rat as a database. For STANDARD and Typhon the number of HHAs overlapped by an alignment is shown for various values of B, the average number of seeds indexed at each position. The columns labeled S show results for STANDARD while the columns labeled T show results for Typhon. For each test the best performing method is shown in bold; we tested seed weights of 10 and 11. HHAs were generated as described in the text by eliminating corresponding annotations with consensus scores <0 There were in total 10 801 HHAs that could potentially be identified for mouse, 852 for fugu and 11 873 for pig. There were 116 exons that could be identified for fugu.