1. Jalview Visualising DAS annotation on Multiple Sequence Alignments help@jalview.org http://www.jalview.org 26 th February 2007 Andrew Waterhouse andrew@compbio.dundee.ac.uk Jim Procter jimp@compbio.dundee.ac.uk

2. Dundee, Scotland. Michele Clamp Broad Institute, USA Geoff Barton James Cuff Harvard, USA Steve Searle Sanger, UK Andrew Waterhouse Jim Procter David Martin Jalview Authors www.vamsas.ac.uk

3. Figure Generation Trees Annotation Features Structures PDB ‘Standard’ Formats FASTA MSF CLUSTAL PILEUP BLC PFAM Distributed Annotation System Distributed Annotation System GFF Jalview Features Newick Secondary Structure Prediction Multiple Sequence Alignment Sequences Alignments Clickable HTML Images Line Art Analysis Consensus Conservation & Clustering Visualization Jalview Annotation

4. eProtein Meeting Jalview + dasobert Released

7. Jalview DAS Client Functionality DAS ANNOTATION SERVERS DAS ANNOTATION SERVERS Query matches ID to Authority Map to local reference frame Mouse over for feature name, links and scores Group features by source Type==colour Highlight start-end Select specific sources Filtered list Add user defined sources

8. Jalview doesn’t do.. Checksum Validation Style Sheets Specific Feature Properties –Currently Supports TYPE, NAME, LINK –Scores To come. Jalview Applet DAS Sequence Retrieval DAS Alignments –Mapping Uniprot2PDB EMBL2Uniprot –Alignment retrieval

9. What We Want From DAS Consistency –DAS specifications (e.g. Range Queries) –Ontology Enable annotation analysis –Compare features from different sources –Feature specific analysis – e.g. ‘DOMAIN’ –Make sense of scores + extra properties Reliability –Registry: Dead Server Detection Last Validated Property –High Volume Queries Come Back Later Bulk Requests