Extract sequence from single OTU 454

[emartinez]

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,

[rhinoceros]

copy&paste it from the file?

[Palecomic]

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.