[EMBOSS] Transeq question, frame phases

[David Mathog]

Test case fasta file
>8Achars
AAAAAAAA

all 6 frames for transeq, standard mode emits:
>_1
KKX
>_2
KKX
>_3
KK
>_4
FF
>_5
FFX
>_6
FFX

But...

AAAAAAAA               Forward
TTTTTTTT                          Reverse
                         abc      cba  <--- codons in diagram
^a^^b^^c^    phase 1   1 KKX    4 XFF
x^a^^b^^c^   phase 2   2 KKX    5 XFF
xx^a^^b^     phase 3   3 KK     6  FF

That is, frames 4->6 are supposed to use, respectively, the same
set of codons as 1->3, but translate on the opposite strand, shouldn't
the number of residues returned be like in the table above, also with
the X at the beginning rather than the end? Or to put it another way,
shouldn't the little "x" bases be ignored on the - strand if they were
also ignored on the +?

Thanks,

David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech