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Jalview Visualising DAS annotation on Multiple Sequence Alignments

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. Geoff Barton. Michele Clamp Broad Institute, USA. David Martin.

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Jalview Visualising DAS annotation on Multiple Sequence Alignments

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

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

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

  4. Jalview + dasobert Released eProtein Meeting

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

  6. 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 Jalview doesn’t do..

  7. What WeWant 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

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