[EMBOSS] Transeq question, frame phases

[Peter]

On Thu, Feb 17, 2011 at 4:30 PM, David Mathog <mathog at caltech.edu> wrote:
>
>
>> Now let's do that with the reverse complement strand:
>>
>> $ transeq asis:TTTTTTTT -filter -frame 1
>> >asis_1
>> FFX

This is what I think that does (forward frames are easy):

Frame 1, so starts at first base:
Letters 123, codon TTT, gives F
Letters 456, codon TTT, gives F
Letters 78, partial codon TT-, gives X

>> $ transeq asis:TTTTTTTT -filter -frame 2
>> >asis_2
>> FFX

Frame 2, so starts at second base:
Letter 1, just T, ignored
Letters 234, codon TTT, gives F
Letters 567, codon TTT, gives F
Letters 8, partial codon T--, gives X

>> $ transeq asis:TTTTTTTT -filter -frame 3
>> >asis_3
>> FF

Frame 3, so starts at third base:
Letters 12, bases TT, ignored
Letters 345, codon TTT, gives F
Letters 678, codon TTT, gives F


> That is the problem.  Let me try to explain more clearly what the issue is.
>
> 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".

I couldn't understand your diagram - probably font spacing issues in part.

The EMBOSS tool is doing all six frames, maybe all you need to work out
the is mapping between its naming and yours.

Note that it can make sense to translate a trailing partial codon, e.g.
TC... could be TCA, TCC, TCG or TCT which all code for S:

$ transeq asis:TCN -filter
>asis_1
S
$ transeq asis:TC -filter
>asis_1
S

Peter