I know most chimeric sequence detecting tools are focused on 16S rRNA sequences. I am wondering whether commands from Mothur can help detect chimeric sequencese from amino acid encoding genes from a soil clone library? If so, what command should I use? Thanks a lot!
chimera.uchime, chimera.perseus, and chimera.slayer(w/ self=T) can be used on any DNA sequences. At this point, nothing in mothur works with translated amino acid sequences. But I don’t know why you’d look for chimeras on anything other than DNA anyway…
Pat
Thanks for your reply! I actually mean functional genes. Once I get rid of chimeric sequences, I need to translate those into amino acids.