Question: Aligning AFLP primers
gravatar for hbw
3.6 years ago by
United States
hbw70 wrote:

I am trying to blast AFLP primer sequences to the genome to find the locations of the AFLP markers. However, I can't seem to find full alignments for the primers on the genome.

For example, in the paper "AFLP fingerprinting of the human genome", Human Genetics,  108(1):59-65, Table 1 reports 100's of location of each primer pair:

Now the MseI primer is GATGAGTCCTGAGTAA. So the M-CAA primer should be GATGAGTCCTGAGTAACAA. When I blast this on the reference human genome at NCBI, the results show the best alignment only covers 6-21 of the query:

    Homo sapiens chromosome 7, GRCh38.p2 Primary Assembly
    Query  6          TGAGTCCTGAGTAACA  21
    Sbjct  148723256  TGAGTCCTGAGTAACA  148723241

However, there should be close to a thousand matches for MseI-CAA across the genome according to the table. Does AFLP not require the whole primer to be matched?

According to the original AFLP paper, "AFLP: a new technique for DNA fingerprinting", NAR 1995, the figure 1, the whole primer is being aligned.

Cross-posted to Biology.SE

markers genetics aflp • 861 views
ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by hbw70
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