Feature inheritance with sequences

[David Martin]

On Fri, 9 Feb 2001, Peter Rice wrote:

> David Martin wrote:
> >
> > One of the great benefits of some of the graphical sequence manipulation
> > tools is that when one chops out a section of a sequence the features
> > travel with it.
> > What is the position with regard to such things in EMBOSS?
> >
> > ie if pasteseq is used to splice sequence a into sequence b, will the
> > feature table travel with it and be updated as well?
>
> An interesting concept.
>
> In principle, yes. Features in EMBOSS follow the GFF model, so they are stored
> as groups of start and end positions. Assuming that they are not one of the
> more exotic kinds of start and end positions, it is easy to 'insert' one
> feature table into another. Deletion is also possible, although ends of
> features within the deleted region rules out making the process completely
> reversible.
>
> I have seen it all before - in the EBI's NEWFEATURES editor when mutating the
> 'replace' qualifiers.

But does it actually work in practice? If one creates a new sequence from
a and b, do the features travel with it?

(I have seen very little documentation on using features.. anyone care to
do a tutorial online via Wiki/IRC at some point as to how features work
in EMBOSS?)

Will EMBOSS write out features as standard in EMBL/Genbank format files or
are we stuck in having extra GFF files floating about..

It would be good to have a tutorial on features.

..d

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