Hi guys,

I’ll keep it as simple as possible, I’ve got a fasta file containing a library of DNA sequences 40 bases in length, This file contains sequences I want to eliminate.

I have another file containing all the sequences I need to eliminate but I can’t find a tool that filters based on sequences themselves, not IDs. I can’t use IDs as they won’t match up.

I think the TN93 tool may be the best option but I’m unsure how to use it properly, I have a clustered fasta file as it requires but it doesn’t seem to work.

Would anyone be able to offer some tips?

(More detail if you wish to read)

I’m a third-year PhD student who recently finished some SELEX protocols and got some sequencing data back.

I have an initial random library and two post-SELEX libraries. In theory every sequence in the original library should be unique, but they’re not, some have as many as 20,000 copies and so have been carried through to the post-SELEX libaries

I wish to eliminate them from the post-SELEX libraries

Cheers

Paul