|
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
|
- 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.
