Hi Jim, I think it would be best if we could discuss these face to face when you are in tomorrow.
Charles Ofoegbu Tochukwu Charles Jalview Visual Analytics Developer/Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK. Skype: cofoegbu www.jalview.org<http://www.jalview.org/> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk/> On 4 Apr 2017, at 17:09, Jim Procter <[email protected]<mailto:[email protected]>> wrote: Thanks for the reply, Charles. On 04/04/2017 14:47, Charles Ofoegbu (Staff) wrote: As I understand it, the query sequence is always first in the alignment (allhits, query.JAL and the template maps) Is that correct ? Yes that is indeed correct. Lawrence - is that also the case for all the alignments generated by the phyre pipeline ? If so, we could add logic to Jalview that defaults to adding annotation to the first sequence in the alignment if 'QUERY' is given as the name, but no sequence is given with that name. Alternately, we have precedent for mapping annotation to sequences by position in the alignment. Much more fragile but equally valid in this case. We could certainly do so. However, doing so would defy the purpose of having the query sequence included in STRUCTMODEL annotation in the first place. Well in that case it could be made optional anyhow. Leaving it empty means Jalview will assume the first sequence is the query (which is what happens when processing other specialised prediction formats). The same assumption could then be made when importing parwise mapping alignments (where we already know what the template sequence ID is because it is also given as a parameter). Furthermore, given that we intend the implementation to be generic enough to support importation of modelled structures from other sources, I reckon that it would be more robust to explicitly define the relationships correctly rather than coding on assumptions. I take your point, but the asumption is only regarding the interpretation of 'QUERY' which is a widely used generic label. j. ps. Thank goodness no one named a gene query! http://www.ensembl.org/Multi/Search/Results?q=query;site=ensembl -- ------------------------------------------------------------------- Dr JB Procter, Jalview Coordinator, The Barton Group Division of Computational Biology, School of Life Sciences University of Dundee, Dundee DD1 5EH, UK. +44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk _______________________________________________ Jalview-dev mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev The University of Dundee is a registered Scottish Charity, No: SC015096
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