Identifying V3V4 region from sequence

Theory behind mothur
1

Hi forum members,

  • I’m working on creating an in-house training set for certain genus. Downloaded data from RDP database. There are few red flags and therefore I would like to confirm if downloaded data has V3V4 region or not.

  • Max length for from available sequences for a genus is 1232 with minimum 500. Removed sequences which had ‘n’ in them.

Can I use pcr.seqs command for to confirm if data set has V3V4 region?

I’d like to perform this excercise on all different genera. One way could be I get V3V4 16s region and blast them. I was unable to find reference 16s region for genera.

Any pointers here would be highly appreciated.

2

Commenting for visibility.
Sorry if I’ve posted in incorrect sub-forum (theory behind mothur, commands in mothur)

3

I would align it against the silva reference alignment and then make sure that everything starts and ends outside of hte V3V4 region.

Pat