[EMBOSS] Needle

[pmr at ebi.ac.uk]

Hi Ryan,

> I have a bunch of protein sequences that are fairly short.  I'm using
> needle to align them.  Occassionally, needle will give me that error
> "Sequence is not nucleic".
>
> I suspect needle is interpreting the sequence as DNA because of its
> content, however they are both protein sequences.  Is there a way I can
> force needle to interpret them as protein sequences?

Yes ... for any sequence input in any program you can use the command line
qualifiers:

-sprotein  if it is protein

-snucleotide (or -snuc) if it is DNA

regards,

Peter