Re: User-defined annotations in Stockholm alignment file

I would absolutely pick the Stockholm format at used in PFAM for that.
It has annotation per alignment (top level), per column, per sequence, etc.

However, the parser currently ignores per-column annotation:
https://github.com/biopython/biopython/issues/357
https://github.com/biopython/biopython/issues/516

For your use case of top-level annotations I think we just need to finish:
https://github.com/biopython/biopython/issues/768
https://github.com/biopython/biopython/pull/769

More eyes on this would help,

Peter

On Sat, Apr 2, 2016 at 2:29 AM, João Rodrigues
<[email protected]> wrote:
> Hi all,
>
> Maybe I'm looking at the wrong format or committing a grave sin, but is it
> possible or acceptable to add annotations to an alignment file in Stockholm
> format? From the current code, custom annotations are ignored upon writing.
> Should I be looking at a different format? FWIW, I'm looking at adding
> e-values to an alignment file.
>
> Cheers,
>
> João
>
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