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Table 4 Effect of the order of releasing enzymes on cDNA-AFLP performance

From: Improved coverage of cDNA-AFLP by sequential digestion of immobilized cDNA

RE 1 RE 2 RE 3 Coverage Redundancy PCR samples Ø Fragment length (nucleotides)
L M H 65 % 38 % 713 226
L H M 65 % 38 % 624 219
M L H 65 % 38 % 672 226
M H L 65 % 38 % 648 226
H L M 64 % 38 % 552 217
H M L 64 % 38 % 552 217
  1. Simulation of cDNA-AFLP with sequential digestion protocol on Arabidopsis RefSeq data was performed using marking enzymes MboI and FatI and six releasing enzymes with different frequencies of occurrence: frequently cutting enzyms H (TasI and MseI), enzymes with a medium frequency of occurrence M (BsaWI and TatI) and infrequently cutting enzymes L (AcyI and CfrI). For each permutation of H, L and M enzyme classes, cDNA-AFLP were simulated for 8 permutations of the releasing enzymes (RE). Average values of coverage, redundancy, PCR effort and fragment length for each permutation of H, L and M were calculated.