[EMBOSS] Needle/water, revcomp

[pmr at ebi.ac.uk]

Clemens Broger writes:

> I have 2 questions:
>
> The first is about identity/similarity in nucleotide alignments made
> with needle (probably the same holds true for water):

Tricky. This requires the matrix to define some codes as ambiguity codes
so we know w-w is not an identity. I woudl guess we can extend the matrix
formats we use to include this information, or perhaps for nucleotide
sequences we can "know" the answer.

I will investigate.

> The second question is about the handling in EMBOSS of
> reverse-complemented nucleotide segments such as
>
> db:seq[10:20:r]
>
> The sequence is first reverse-complemented and then residues 10 to 20
> are cut out.
> Biologists usually expect that residues 10 to 20 are first cut out and
> then reverse-complemented.
>
> Can this be changed? That would be very helpful.

Oops. Yes - will do.

regards,

Peter Rice