Table 2.
Restriction enzymes used for simulations
| Restriction enzyme | Recognition site | Occurrence in RefSeq EST sets (%) | |||
| Arabidopsis thaliana | Homo sapiens | Mus musculus | |||
| 1 | MboI | ▼GATC | 97.2 | 98.8 | 82.5 |
| 2 | HpaII | C▼CGG | 84.4 | 93.3 | 64.7 |
| 3 | HinP1I | G▼CGC | 60.3 | 89.4 | 61.7 |
| 4 | Csp6I | G▼TAC | 87.9 | 97.5 | 81.4 |
| 5 | TaqI | T▼CGA | 95.3 | 89.4 | 64.2 |
| 6 | TasI | ▼AATT | 97.5 | 98.2 | 80.2 |
| 7 | MseI | T▼TAA | 96.3 | 97.2 | 78.9 |
| 8 | FatI | ▼CATG | 96.4 | 99.7 | 83.5 |
| 9 | MaeI | C▼TAG | 88.6 | 95.1 | 76.3 |
| 10 | MaeII | A▼CGT | 86.7 | 92.0 | 64.8 |
| 11 | ApoI | R▼AATTY | 82.7 | 86.2 | 68.5 |
| 12 | BstYI | R▼GATCY | 80.0 | 90.5 | 70.4 |
| 13 | AcyI | GR▼CGYC | 37.8 | 70.3 | 46.4 |
| 14 | BmeT110I | CY▼CGRG | 49.6 | 79.3 | 52.8 |
| 15 | Cfr10I | R▼CCGGY | 49.6 | 68.6 | 45.1 |
| 16 | CfrI | Y▼GGCCR | 45.3 | 90.3 | 68.7 |
| 17 | BsaWI | W▼CCGGW | 64.1 | 60.1 | 44.2 |
| 18 | TatI | W▼GTACW | 63.5 | 86.8 | 72.7 |
All these restriction enzymes are commercially available, supplying companies can be found on the REBASE [23] homepage. Frequency of occurrence in EST sets were calculated using NCBI Reference Sequence collections without repetition, sequences containing more than one copy of a recognition site counted only once.