[EMBOSS] Transeq question, frame phases

[Peter]

On Wed, Feb 16, 2011 at 8:54 PM, David Mathog <mathog at caltech.edu> wrote:
> 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
>

Note you can do that with a single command line:

$ transeq asis:AAAAAAAA -filter -frame 6
>asis_1
KKX
>asis_2
KKX
>asis_3
KK
>asis_4
FF
>asis_5
FFX
>asis_6
FFX

Note that while using 1, 2, 3 for the forward frames is well defined, there
are two conventions for the reverse frame - do you start from the left or
the right?

First let's just do the forward frames,

$ transeq asis:AAAAAAAA -filter -frame 1
>asis_1
KKX
$ transeq asis:AAAAAAAA -filter -frame 2
>asis_2
KKX
$ transeq asis:AAAAAAAA -filter -frame 3
>asis_3
KK

Are you happy with them?

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

Now let's do that with the original sequence but the negative frames:

$ transeq asis:AAAAAAAA -filter -frame -3
>asis_6
FFX
$ transeq asis:AAAAAAAA -filter -frame -2
>asis_5
FFX
$ transeq asis:AAAAAAAA -filter -frame -1
>asis_4
FF

Same results - perhaps the naming isn't as you expected?

Peter