Table 1 Illustration of the Ampsig format with example values
From: A format for databasing and comparison of AFLP fingerprint profiles
# | Field | Example Value | Information |
|---|---|---|---|
1 | Technique | AFLP | Full abbreviation of type of DNA markers, such as AFLP, SSR, RAPD |
2 | Experiment | EcoRI_ACA-MseI_CAC | For VNTR, RAPD and SSR markers, primer sequences will be given in full. In this example, a six-nucleotide cutting enzyme EcoRI and a four-nucleotide cutting enzyme MseI were used to digest genomic DNA. PCR reaction was conducted with an EcoRI primer with selective nucleotides ACA, and a MseI primer with selective nucleotides CAC |
3 | Source | D Sonia id0011 | Biological source of DNA. The binomial system with abbreviation of genus followed by species name is used to designate biological species. It is followed by a four-digit ID number to identify individual samples. In this example, DNA was isolated from a plant belonging to genus Dendrobium, species Sonia, with a lab-assigned ID 0011 |
4 | UnitSize | 1 | Unit size of DNA fragment to define the unit spacing. It can also be interpreted as the sequence resolution. In this example, the 1 indicates that the sequence spacing is 1 base pair. |
5 | StartSize | 50 | Size of the first DNA fragment (in base pairs) |
6 | EndSize | 90 | Size of the last DNA fragment. This field is redundant, and is kept mainly for proof-reading |
7 | Annotation | AFLP profile for D. Sonia | Annotation of the fingerprint (only if required) |
8 | Signature | A..B..DC..B.D.....CC...A.....DDA.A....C..D..BB | Alternatively, a system employing the symbols [4, 3, 2, 1] for peaks and [0] for peak-absence may also be used. |