Filter out a specified sequence

Since some 16S primer sets amplify mitochondrial and chloroplast DNA and it is usually desirable to filter these out, it would be nice if Mothur had a feature where a sequence to be filtered out can be entered (for example, the known mtDNA sequence for arabidopsis). The sequence is then BLASTed against the data set you are working with. You could then input a sequence similarity cutoff (to account for homopolymers, etc.) before the sequence is filtered out.

I hear you - one way that you can do this would be to classify your sequences and find those that classify as mt and cp DNA. Then take those sequence names and make an accnos file (just a list of sequecne names) and then use that file with remove.seqs to remove the offending sequences.

Let us know if you try that and how it works out…

hye, once you align sequences, you would get report file, eliminating sequening with low search score score and alignment length served my purpose well.
may be you could also have a try