So - last week, Lawrence Kelley and spent around 3 days hacking a prototype link between phyre2 and Jalview. Here's the story so far:
Our aim is to provide Jalview users a link to submit sequences to Phyre2, and also allow Phyre2 users to open their model results in Jalview. The former requires extension of Jalview's existing REST service interface and some subtle modifications of the Phyre2 server. The latter (which also blocks the former), involves deciding how a set of models derived from a set of template sequences (each with their own sequence and dataset associations) can be shown aligned to the user's Query sequence and the multiple sequence alignment used to discover templates and create the models. Things aren't quite ready for public consumption, but here's what is now in the repository: * phyre2 spike branch - special build for launching Jalview from a phyre2 result page - button is only shown when my dundee email used for input). * Patches on the branch - new STRUCTMODEL statement in annotation file This allows specification of a Query sequence, a template seuqence name, and URI's for a PDB file and pairwise alignment that provide the model coordinates (pdb file with sequence matching query, but coordinates from template structure), and alignment between query and template - various minor patches to make the prototype work ... see git log Current procedure for viewing phyre2 results: Phyre2 provides query.jal and query.jal.ann - the profile MSA for the query (including indels) and an annotation file. Loading query.jal, and dropping query.jal.jvannot should result in: * The query sequence set as reference for alignment, and insertions hidden * scores from psi-blast added as annotation to profile sequences (access via Calculations->Sort->...) * models and pairwise alignments are retrieved via STRUCTMODEL statement i. Models are associated with query sequence - can view all models by: 1. Select "View 3D Structure ..." after right clicking on query sequence's sequence ID. 2. Select 'Cached structures' from the dropdown menu at top of 3d structure dialog - this should show all the models loaded onto the alignment. 3. pick one or all models, and hit 'View' - the models should be displayed superimposed. Outstanding implementation: * template sequences need to be added to the query/profile MSA according to the provided pairwise alignment (Jim working on this code) * Model PDB files need to mapped to template sequences according to provided pairwise alignment (Tochukwu - this is something you could look at ...) * Each model is associated with both the Query sequence AND the template sequence added to the alignment - which is not normally the situation in Jalview. We will need to come up with solutions (UI, datamodel extensions, etc) that allows models to be coloured according to properties derived from either the modelling process, the query/template alignment, or annotation derived from the template sequences. That's all for now.. see you next week (if not before via Skype!) Jim -- ------------------------------------------------------------------- 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
