[Jalview-discuss] renumbering protein sequences - working with domains not whole chains

[James Procter]

Ffenics wrote:
> 
> Hi there .. I'm currently investigating how to use Jalview and DAS to 
> annotate functional residues in protein domains. I give Jalview my own 
> multiple protein sequence alignments.
> 
> A given protein sequence in the alignmment may, or may not,  include the 
> whole of a protein chain.. Because I won't always be using a whole 
> protein chain,  is there a way of mapping the residue numbering as 
> contained in the pdbs of these protein domains with the multiple 
> sequence alignment in Jalview?
If you right click on a sequence and follow the Structure->Associate 
Structure submenu you can select 'From file' to load your own PDB file 
onto the sequence. Jalview will map the residues in the structure to the 
displayed sequence via a global pairwise alignment.

Unfortunately, there is no way, currently, to do this in bulk - i.e. say 
'associate all the pdb files in this directory to their closest homologs 
in the alignment'. This is a feature which we hope to implement some 
time in the future.

> Might I be able to achieve this by mapping each sequence to its 
> associated protein domain  (which I can provide as a pdb file) or is 
> there another way to do this (if its possible at all).
If your proteins are in Uniprot, the easiest way is to name your 
sequences with their Uniprot IDs.  The 'Fetch DB Refs' function under 
the web service menu will then correct the start/end numbering against 
the uniprot record, and add any PDB cross references automatically. This 
at least means that you can view DAS features via the uniprot coordinate 
system. The latest development version of jalview also supports PDB ids 
as a coordinate system (enabling the two or three DAS services which 
support PDB id queries such as the dssp service).

Is that what you mean ?

Jim.

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J. B. Procter  (ENFIN/VAMSAS)  Barton Bioinformatics Research Group
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