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  • Extract sequence from single OTU 454

    Hi everyone,

    I would like to extract a single sequence corresponding to an OTU obtained in the analysis of the 454 pyrosequence.

    Exemple:
    I have found by RDP pyrosequencing analysis than an 40% of the reads are a specific genera. I would like to obtain the SEQUENCE of this genera to compare it with other sequences from genbank.

    Maybe is easy, but I cannot manage it so far.

    More info: I used for the analysis MOTHUR and RDP.

    Thank you,

  • #2
    copy&paste it from the file?
    savetherhino.org

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    • #3
      Hi emartinez,

      in Mothur you need to use the Get.oturep command: http://www.mothur.org/wiki/Get.oturep which gives you a single sequence per OTU. You might want to check out the weighted parameter too, depending on how you've trimmed and preprocessed your reads.

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