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  • microsatellite query

    Hello wise people!

    I have approx 10,000 microsatellites that I obtained from some assembled dna of a non-model organism. I selected a subset of the microsatellites including 50bp of the right and left flanking sites.
    My intent is to use this subset as a query to search in sequenced dna data from a number of sample populations and see if I can find similar sequences in the different popns.

    I am trying to think of a way to do this, does anyone know of a program/software (or a combination of different programs) that can achieve this? For those who use CLC gwb, any ideas?
    I was thinking of mapping each popn to the microsatellite+flanking seqs (use the microsatellite seqs as reference), extracting a consensus sequence, then aligning that sequence back to the microsatellite seq. Is that a good way or what?
    Please help...

  • #2
    Out of curiosity, can you please tell me how you identified the microsatellite regions? Any specific tool or method?

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    • #3
      Originally posted by vivek_ View Post
      Out of curiosity, can you please tell me how you identified the microsatellite regions? Any specific tool or method?
      I found a program online called phobos, that's the one I used. There is also TRF and msat commander but I haven't tried using those ones yet.

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      • #4
        How large is your subset that you want to investigate?

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        • #5
          Originally posted by NGS_New_User View Post
          I found a program online called phobos, that's the one I used. There is also TRF and msat commander but I haven't tried using those ones yet.
          Thanks for that. TRF seems to have been used in the 1000 genomes analysis as well.

          Comment


          • #6
            Originally posted by JackieBadger View Post
            How large is your subset that you want to investigate?
            I am first starting with a small group ie 10 sequences, each sequence is approx 150bp (ie the left flank region + repeat motif + right flanking region). The size of one of the popns that I want to search in is approx 1.8million sequences.

            Comment

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