Table 3 Comparison of cDNA-AFLP protocols
From: Improved coverage of cDNA-AFLP by sequential digestion of immobilized cDNA
Origin of EST | Protocol | Marking enzyme | Releasing enzyme | Sequence coverage | Sequence redundancy | Fragment length (nucleotides) |
|---|---|---|---|---|---|---|
Arabidopsis thaliana | Single pair of enzymes | TaqI | TasI | 49 % | 0 % | 209 |
Double pair of enzymes | FatI | TasI | 65 % | 29 % | 203 | |
MboI | MseI | |||||
Sequential digestion | FatI (A) | MboI (1), TasI (2) | 75 % | 25 % | 179 | |
MboI (B) | FatI (3), TasI (4) | |||||
FatI (A) | MboI (1), MseI (2), TasI (3) | 78 % | 30 % | 183 | ||
MboI (B) | FatI (4), MseI (5), TasI (6) | |||||
Flip/Flop | FatI | MboI | 64 % | 0 % | 155 | |
MboI | FatI | |||||
Mouse | Single pair of enzymes | MboI | MseI | 54 % | 0 % | 230 |
Double pair of enzymes | MboI | TasI | 75 % | 32 % | 230 | |
Csp6I | TaqI | |||||
Sequential digestion | MboI (A) | Csp6I (1), FatI (2) | 85 % | 35 % | 258 | |
Csp6I (B) | MboI (3), FatI (4) | |||||
MboI (A) | Csp6I (1), MseI (2), FatI (3) | 87 % | 41 % | 270 | ||
Csp6I (B) | MseI (4), MboI (5), FatI (6) | |||||
Flip/Flop | MboI | Csp6I | 75 % | 0 % | 211 | |
Csp6I | MboI | |||||
Human | Single pair of enzymes | HinPI | MseI | 61 % | 0 % | 260 |
Double pair of enzymes | MboI | MseI | 76 % | 33 % | 223 | |
Csp6I | TaqI | |||||
Sequential digestion | MboI (A) | FatI (1), Csp6I (2) | 82 % | 31 % | 249 | |
Csp6I (B) | MboI (3), FatI (4) | |||||
MboI (A) | Csp6I (1), HinPI (2), FatI (3) | 85 % | 35 % | 274 | ||
Csp6I (B) | MboI (4), FatI (5), HinPI (6) | |||||
Flip/Flop | MboI | Csp6I | 76 % | 0 % | 228 | |
Csp6I | MboI |