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  • Online Bisulfite Alignment programs?

    Hello,

    this is my first time posting here. I was wondering if you could help me find an online free alignment program that could handle short bisulfite alignments.

    I do not need to do automated alignment of a large batch of sequences, just align a handful (~20 or so) of 50bp sequences against the whole genome. I know about BSMAP, Novoalign, and other whole genome Bisulfite mapping programs, but I am not able to download any software right now, and just need to check something quickly. E.i. I need something like NCBI Blast that I could use online without downloading anything first.

    Thanks a lot!

    L.

  • #2
    Hi there,

    if you just need a one-off answer you can send me a list of sequences to [email protected] (in FastQ or FastA format) and I can send you the results back via email.

    Best,
    Felix

    Comment


    • #3
      Thanks for the offer, felix!

      So there really isn't an online free alignment software?

      Comment


      • #4
        Well there is something which is pretty much what you asked for: http://medgen.ugent.be/methBLAST/
        I never used it myself, but maybe it is useful for you. But if I were you I would try to get it done with one of the software you mentioned or bismark which Felix offered you.

        Comment


        • #5
          Check out the RMAP developed by Andrew Smith at the link below:

          Comment

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