EMBOSS cusp for individual fasta sequences

Question

[Daniel]

Is it possible to run the EMBOSS cusp program so that it gives output (codon usage) for each individual sequence in a list of FASTA sequences? In the default version it analyzes all sequences together.

[Daniel]

In contrary to EMBOSS cusp, the EMBOSS geecee program processes each individual sequence from a list of fasta sequences.

Answer 1

[Neilfws]

From the cusp documentation:

If multiple sequences are input then the statistics are given for all of the sequences together, not individually.

So no, this is not an option in the command-line arguments. You will have to split your multiple FASTA sequence file into individual sequences. Lots of ways to do that, one of them is EMBOSS seqretsplit.

[Daniel]

How would this be applicable in a Galaxy workflow? We start with a list of FASTA sequences and we want to run "cusp" on each of them.