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: enter image description here

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. enter image description here

Cross-posted to Biostars.

Update: One needs to use the digestion enzyme recognition site to map the AFLP markers. Example: http://insilico.ehu.es/AFLP/info.html

  • $\begingroup$ @TalhaIrfan please see these guidelines on tags - you've been adding a lot of very narrow and new tags $\endgroup$ – rg255 Jun 6 '16 at 6:55
  • $\begingroup$ @rg255 Thanks RG! I would dare to disagree a bit and I still believe Biology SE needs more tags (I haven't added any of tag blindly). Like BCI wasn't even a tag week ago. Similarly ncRNA and lncRNA must be tags as many researchers want to work with them. GRCh37 and GRCh38 maybe narrow to biologists, but they are important for a bioinformatician. $\endgroup$ – Failed Scientist Jun 6 '16 at 11:40
  • $\begingroup$ @rg255 Having said that, I have still revised the guidelines in order to ensure I am serving the community. Thanks again! $\endgroup$ – Failed Scientist Jun 6 '16 at 11:42
  • $\begingroup$ Just that things like ncrna and lncrna are likely to be better served under a more broad tag like rna or noncoding-rna - people don't follow hundreds of tags but may subscribe to a handful of favorites (e.g. I follow evolution but wouldn't follow the tag evolution-in-the-jurassic-period if it existed) $\endgroup$ – rg255 Jun 8 '16 at 6:36

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