Skip to main content

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    
  1. cDNA-AFLP protocols were simulated with MECS software on Arabidopsis, mouse and human RefSeq ESTs. For the sequential digestion strategy, the order of marking enzymes (A, B) and releasing enzymes (1 to 6) is specified (see Fig. 1 for details).