Table 1.
Use of Autofinish on University of Washington Projects during 1998 and 1999
| Project | No. of finishing reads | No. of Autofinish reads (% Autofinish reads) |
|---|---|---|
| djs201 | 267 | 161 (60%) |
| rg391h05 | 390 | 236 (61%) |
| djs104 | 140 | 90 (64%) |
| djs259 | 148 | 103 (70%) |
| PAO1 | 1637 | 1195 (73%) |
| djs333 | 141 | 112 (79%) |
| djs119 | 82 | 66 (80%) |
| djs228 | 128 | 104 (81%) |
| djs362 | 99 | 82 (83%) |
| djs146 | 141 | 121 (86%) |
| djs94 | 127 | 111 (87%) |
| djs327 | 173 | 156 (90%) |
| djs77 | 113 | 107 (95%) |
| djs306 | 192 | 183 (95%) |
| djs124 | 149 | 145 (97%) |
| djs301 | 224 | 219 (98%) |
| djs14 | 91 | 91 (100%) |
| djs40 | 11 | 11 (100%) |
| djs45 | 66 | 66 (100%) |
| djs58 | 72 | 72 (100%) |
| djs292 | 86 | 86 (100%) |
Autofinish (versions 5.0 to 9.0) was used on these projects at the University of Washington during 1998 and 1999. All are 150-kb to 200-kb BACs except for PA01, the six-megabase Pseudomonas aeruginosa bacterial genome. Immediately after shotgun, Autofinish was run for three rounds on each project: Each time, the lab made the reads suggested by Autofinish (without adding or removing any suggested reads) and reassembled the project. After this, if the project was still not finished, a human finisher manually completed the project. All of these projects have been submitted to GenBank as Phase 3 Complete sequence. (No. of finishing reads) The sum of Autofinish-selected reads and human-selected reads. (No. of Autofinish reads [% Autofinish Reads] The number and percentage of finishing reads that were suggested by Autofinish.