Selectively Amplified Microsatellite Polymorphic Loci
Selective amplified microsatellite polymorphic loci (SAMPL) analysis (Witsenboer et al.,1997) is a modification of AFLP methodology. The selective amplification uses one of the AFLP endonucleases in combination with a primer. The SAMPL primer essentially comprises of a sequence repeated a few times along the genome studied, as for example microsatellite-like sequences.
SAMPL is used for genotyping of eukaryotic organism, mostly plants. In this service we have included SAMPL in order to allow learning the usage of the technique, so that the porpose is mostly educational. As repeated sequences along prokaryotic genomes are unusual in many species, we have search for 15 mer long oligonucleotides with at least 8 copies in each prokaryotic genome. Those oligonucleotides may be used to simulated SAMPL in prokaryotes, but their design as PCR primers has not been checked (they are provided to allow learning fo the technique). The service will only show the oligonucleotides on request.
Concerning endonucleases, the list includes only the ones yielding overhand ends, which may be ligate to adaptors. In order to help the user, the number of times the selected endonuclease cleaves main chromosome of the selected prokaryote is shown.
The technique may be applied to prokaryotic genotyping, but to our knowledge, the theoretical method proposed in this service has not been tried in the lab.
Witsenboer, H., Michelmore, R. W., and Vogel, J. (1997). Identification, genetic localization, and allelic diversity of selectively amplified microsatellite polymorphic loci in lettuce and wild relatives (Lactuca spp.) Genome 40: 923-936
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