[Jalview-discuss] numbering system
jimp at compbio.dundee.ac.uk
Mon Dec 1 12:12:59 GMT 2008
Hello Luciane - I'm glad you got your subscription/posting issue sorted out!
Vieira de Mello, Luciane wrote:
> I am making a figure using Jalview of my sequence alignment. The first 68
> residues are part of the pro-enzyme. So, I would like to start to
> numbering the
> sequence from residue 69 (mature protein), but calling it residue 1. Can
> do it?
There's currently no direct or automatic way of doing this. Jalview is
hard-coded to automatically change the numbering of a sequence to match
the external database record (such as Uniprot or EMBL), rather than
preserve the local numbering and match back. But this is really only
important for feature retrieval and display. Would it be sufficient to
simply add a row of alignment annotation corresponding to the sequence
mature numbering 1234567
You could create an annotation file to do this quite easily (see
http://www.jalview.org/help/html/features/annotationsFormat.html ) - so
the numbering would at least appear on the diagram. Remember that you
would probably need to skip some of the numbers in order to ensure the
scale is legible.
also, can Jalview work with negative numbers from residue 1 of the
> sequence till residue 68 (for the pro-enzyme)? If not can I edit the
> numbers as
> for example, 1P, 10P, 20P..... 60P, and then start from 1 again from the
Jalview is probably never going to work explicitly with negative
sequence positions. Furthermore, the 1P,10P style of position labelling
is also probably not likely to be implemented explicitly. Except perhaps
for constructing labels like this to attach to alignment column
positions (which you could do with alignment annotation). Jalview also
simulates this kind of numbering to show the exact residue number +
insertion code for a mapping of amino acid positions to a PDB structure
using the sequence features. If you need to find out where you are in
the sequence whilst working with the alignment in Jalview, rather than
generating numbered positions for a figure, then you could do this for
your case: create a features file with features where the description
text gives the position in the uniprot sequence (or the local alignment
sequence). However, remember that these numbers would then only be a
label displayed when the mouse hovers over the mapped position, not an
actual numbering system used for displaying external features, or
something that is displayed if the alignment is exported as PNG or EPS.
> Hope this is clear.
It is! I hope my responses are too - sorry there was no short and easy
answer to this, but I hope you'll be able to make some kind of diagram
using an annotation file.
J. B. Procter (ENFIN/VAMSAS) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.
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