Feature inheritance with sequences

Peter Rice Peter.Rice at uk.lionbioscience.com
Fri Feb 9 14:58:29 UTC 2001

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

I have seen it all before - in the EBI's NEWFEATURES editor when mutating the
'replace' qualifiers.

Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723

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