I tried chimera.uchime and I have a question about the database mode:
I tried the reference data base mode with the rRNA16Sgold-database from chimera slayer.

Can chimera.uchime recognize letters like y and n in the gold-database or can it only read sequences containing only acgt?


I’m pretty sure it just treats non-ATGC’s as N’s.


I´m just asking because I also used the stand-alone version of uchime and I get something like this as an output for the alignment of chimeras and parents:

ParentA aGGAATTy
The uchime-usearch version seems not to do that. That is why I was wondering which version the mothur package uses.

When I analyse my data I get the same results for the mothur package and the uchime-standalone version (which seems not to recognize other letters)

The chimera.uchime command in mothur is just a wrapper for the uchime program written by Robert C. Edgar, We use the latest version the uchime source, uchime4.2.40_src.tar.gz, to build the executable version of uchime we release with mothur.