Hi Lawrence, Hope this email meets you well. We have made some progress with the Jalview-phyre2 integration. As you are aware, the following use cases were identified in the Jalview-Phyre2 collaboration document:
1. Phyre2 users wanting to use Jalview 2. Jalview users wanting to use Phyre2 I have pushed an initial prototype for the first use case to Jalview's Phyre2 spike branch. A brief summary of the features enabled is outlined further below. There are some other features that would be best demonstrated. Accordingly, I think it is now time for us to have a look at it together via Skype when Jim is back (Jim is away this week and should be back on Monday). This will also enable us to obtain very useful feedback from you. The current state of the implementation provides a good foundation for the second use case, which is yet to be implemented. I hope to commence implementation for Phyre2 Job submission and management from Jalview very soon. Once these are completed, it should plugin easily into the current implementation in such a way as to realise the second use case. Furthermore, there are some changes required on Phyre2 server end, and I have summarised them under change request section below. Features Enabled in the Current Prototype * Support for loading Phyre2 result alignment with custom Jalview annotation file generated by Phyre2 * Detailed interactive sequence/structure display * Linking of the template sequences to their 3D structure models on importing the annotation file * Structure <--> Sequence mapping using the original fasta pair-wise alignment file generated by Phyre2 * Superposing, viewing and comparing two or more modelled structured * Transfer of features and annotations from the modelled 3D structures onto their template sequence when viewed Change Request Changes to Phyre2 server 1. The outset alignment file to be opened by the generated launchapp.jnlp Jalview file should be changed from “query.jal” to “allhits.fasta” 2. For the sake of consistency, “query.jal.ann” should be rename to “allhits.jal.ann” since the “allhits.fasta” alignment file is made the outset input alignment. 3. Drop custom mapping files specifically generated for Jalview (i.e “xxx.fasta.jal”) Changes to the generated Jalview annotation file 1. Modify the file accordingly to reference the original Phyre2 fasta mapping files generated rather than the custom ones stated in point three above 2. Replace the name “QUERY” in STRUCTMODEL annotations with the actual name of the Query Sequence 3. Make enhancement to the file to incorporate HEADER_STRUCT_MODEL annotation. See notes below: HEADER_STRUCT_MODEL annotation: * The HEADER_STRUCT_MODEL annotation has been introduced to enable dynamic definition of the data columns for the STRUCTMODEL annotation. * The HEADER_STRUCT_MODEL should be tab-delimited just like STRUCTMODEL * The HEADER_STRUCT_MODEL should be declare once, and MUST be declared before the first instance of STRUCTMODEL * Each column of the HEADER_STRUCT_MODEL defines the corresponding columns in the STRUCTMODEL annotations * The first four columns of HEADER_STRUCT_MODEL (QUERY_SEQ, TEMPLATE_SEQ, MODEL_FILE, MAPPING_FILE) are compulsory and MUST be provided in the given order. * Data in STRUCT_MODEL can be formatted as HTML (as long as it contains no tab character) * Current implementation in Jalview enables backward compatibility - older “.jal.ann” annotation files generated by Phyre2 server can still be processed. * Infinite number of additional meta-data column can subsequently be included in any order. For instance the meta-data from the “crudlist" should be added to the annotation file as follows: HEADER_STRUCT_MODEL QUERY_SEQ TEMPLATE_SEQ MODEL_FILE MAPPING_FILE Confidence % I.D Aligned Range Other Information STRUCTMODEL FER_CAPAN c4n58A_ c4n58A_.1.pdb c4n58A_.1.fasta 1 54 48-143 <b>PDB Header: </b>Hyrolase<br><b>Chain: </b>A STRUCTMODEL FER_CAPAN d1a70a_ d1a70a_.2.pdb d1a70a_.2.fasta 1 71 48-144 <b>Fold: </b>Beta-Grasp (ubiquitin-like) Please let me know if you find anything unclear regarding the requested changes. Apologies for the lengthy mail! Best regards, 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/> The University of Dundee is a registered Scottish Charity, No: SC015096
_______________________________________________ Jalview-dev mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev
