1 Integrated Genome Browser User’s Guide February 2007 IGB User’s Guide 1 2 Table of Contents GETTING STARTED.................................................................................................................... 7 Introduction......................................................................................................................7 Overview of IGB functionality.................................................................................... 7 Unique features and benefits of IGB........................................................................... 7 Finding documentation and source code..........................................................................8 Document conventions.....................................................................................................8 Installation........................................................................................................................9 System requirements....................................................................................................9 Typical installation using Java Web Start....................................................................9 Advanced installation.................................................................................................10 Launching IGB...............................................................................................................10 Launching using Java Web Start................................................................................10 Other choices............................................................................................................. 11 GETTING FAMILIAR WITH IGB..................................................................................................12 Terminology...................................................................................................................12 Genomes and chromosomes...................................................................................... 12 Annotations, sequences and graphs........................................................................... 12 The main window.......................................................................................................... 13 The title bar................................................................................................................13 The status bar............................................................................................................. 14 The viewer................................................................................................................. 14 Annotations................................................................................................................15 Track handles.............................................................................................................15 Zoom sliders and scroll bars...................................................................................... 16 The hairline position marker......................................................................................16 Tabbed panels............................................................................................................ 16 The console................................................................................................................ 17 Navigation......................................................................................................................17 Choosing a genome and chromosome....................................................................... 17 Zooming and scrolling horizontally...........................................................................18 Zooming and scrolling vertically...............................................................................18 Going to a specific coordinate................................................................................... 19 Bookmarks................................................................................................................. 20 Clearing the view....................................................................................................... 20 Advanced navigation................................................................................................. 20 Selecting items with a mouse.........................................................................................20 Zooming to selected items......................................................................................... 21 Customization................................................................................................................ 21 Opening tab panels in new windows......................................................................... 21 Keyboard shortcuts.................................................................................................... 22 Customizing display properties..................................................................................22 IGB User’s Guide 2 3 Setting preferences.....................................................................................................22 LOADING ANNOTATIONS...........................................................................................................23 Data sources...................................................................................................................23 Loading annotations from QuickLoad...........................................................................23 Loading annotations from DAS servers.........................................................................25 Loading from DAS/1................................................................................................. 25 Loading from DAS/2................................................................................................. 26 Loading annotations from files...................................................................................... 28 Merging with current genome....................................................................................29 Viewing in a new genome..........................................................................................30 Annotation file formats..............................................................................................30 Details for selected features...........................................................................................31 Links to public web sites................................................................................................31 WORKING WITH SEQUENCE RESIDUES......................................................................................... 33 Loading sequences.........................................................................................................33 Loading from QuickLoad.......................................................................................... 33 Loading from a DAS server.......................................................................................33 Loading from a file.................................................................................................... 34 Viewing sequence residues............................................................................................35 Copying sequence bases................................................................................................ 36 SEARCHING............................................................................................................................37 Finding an annotation by name......................................................................................37 Browsing for annotations...............................................................................................37 Finding sequence patterns..............................................................................................38 Finding instances of a known sequence.....................................................................39 Finding instances of a sequence containing unknowns............................................. 40 Clearing pattern search results...................................................................................41 CUSTOMIZING ANNOTATION TRACKS...........................................................................................42 Changing the width of track handles............................................................................. 42 Re-ordering tracks top-to-bottom ................................................................................. 42 Selecting tracks.............................................................................................................. 43 Changing track properties..............................................................................................43 Changing annotation colors........................................................................................... 44 Changing track names....................................................................................................44 Hiding and showing annotation tracks...........................................................................44 Hiding and showing strands...........................................................................................44 Collapsing and expanding tracks................................................................................... 45 Setting a row limit .........................................................................................................45