Blixem User Manual

• Revision History
  • Introduction
    • An aside about the name “Blixem”
      • Getting Started
        • Running Blixem
          • Input files
            • GFF file
              • Transcripts
                • Variations
                  • Sample GFF file
                    • FASTA file
                      • Combined GFF and FASTA file
                        • Configuration file
                          • Program defaults
                            • Fetch methods
                              • Data types
                                • Source mapping
                                  • Sources
                                    • User settings
                                      • Colour key file
                                        • The Blixem Window
                                          • Active Strand
                                            • Big Picture
                                              • Bumping the transcript view
                                          • Detail View
                                            • Match colours
                                            • Alignment lists
                                            • Nucleotide mode
                                            • Protein mode
                                            • Exons
                                          • Coverage view
                                          • The toolbar
                                          • The main menu
                                          • Hiding sections of the window
                                          • Operation
                                            • Navigation
                                              • Scrolling
                                                • Zooming
                                                  • Selections
                                                    • Selecting sequences
                                                    • Selecting coordinates
                                                    • Finding sequences
                                                    • Copy and paste
                                                  • Sorting alignments
                                                  • Fetching sequences
                                                    • Grouping sequences
                                                      • Creating a group from a selection
                                                      • Creating a group from a search
                                                      • Creating a temporary match-set group from the current selection
                                                      • Editing groups
                                                    • Running dotter
                                                      • Reference sequence versus itself
                                                        • Dotter HSPs only
                                                          • Settings
                                                            • Features
                                                            • Highlight variations
                                                            • Show polyA tails
                                                            • Show Unaligned Sequence
                                                            • Show Colinearity Lines
                                                            • Show Splice Sites
                                                            • Highlight Differences
                                                              • Squash Matches
                                                                • Display
                                                                  • Use print colours
                                                                    • Font
                                                                      • %ID per cell
                                                                        • Max %ID
                                                                          • Min %ID
                                                                            • Depth per cell
                                                                              • Columns
                                                                                • Load optional data
                                                                                • Column settings
                                                                              • Appearance
                                                                            • Key
                                                                          • Keyboard shortcuts