> Now let's do that with the reverse complement strand:
>
> $ transeq asis:TTTTTTTT -filter -frame 1
> >asis_1
> FFX
> $ transeq asis:TTTTTTTT -filter -frame 2
> >asis_2
> FFX
> $ transeq asis:TTTTTTTT -filter -frame 3
> >asis_3
> FF
That is the problem. Let me try to explain more clearly what the issue is.
AAAAAAAA Forward
TTTTTTTT Reverse
abc cba <--- codons in diagram
^a^^b^^c^ phase 1 1 KKX 4 XFF EXPECTED
x^a^^b^^c^ phase 2 2 KKX 5 XFF EXPECTED
xx^a^^b^ phase 3 3 KK 6 FF EXPECTED
^a^^b^^c^ phase 1 1 KKX 4 FF OBSERVED
x^a^^b^^c^ phase 2 2 KKX 5 FFX OBSERVED
xx^a^^b^ phase 3 3 KK 6 FFX OBSERVED
Assume an extra codon L to the left of a.
abc baL <--- codons in diagram
^a^^b^^c^ phase 1 1 KKX 4 FF EXPLAINED?
^^a^^b^^c^ phase 2 2 KKX 5 FFX EXPLAINED?
L^^a^^b^ phase 3 3 KK 6 FFX EXPLAINED?
That is, if the meaning of the + phases is to define the three codons
a,b,c as shown in the diagram, such that the forward translation is as
shown, then the reverse translation should be as shown above in
expected. That is, it is the translation of the exact same set of
codons done individually, but for the - strand reverse complement the
codon first, and then invert the resulting translated sequence. That
way the X, where it occurs is attached to the same partial codon "c".
What I think is happening in transeq is that it is starting with the
first full codon in the frame on the given strand. In effect that
shifts the translated codons as shown in the "EXPLAINED?" section.
If partial codons were not translated then these would all be equivalent.
Regards,
David Mathog
[email protected]
Manager, Sequence Analysis Facility, Biology Division, Caltech
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