GENtle/Sequence map

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GENtle splash screen.png The GENtle manual

About - FAQ - Setup - DNA - Protein - PCR and Primer Design - Sequencing - Alignments - Calculators - Virtual Gel - Image Viewer - Tools and Dialogs - Web interface - Graphs and plots - DNA map - Sequence map - Dot plot - Restriction Identifier

The sequence map.

The sequence map is used by most GENtle modules. It shows sequences of DNA or amino acids, as well as primers, features, restriction sites and more. The basic behaviour, however, is always similar.

Clicks[edit]

A double click usuaqlly opens the editor for the sequence.

Context menu[edit]

The available functions in the context menu vary with the module the sequence map is used in, its state, and selection.

Edit sequence Turn on edit mode
Transform sequence Invert and/or complement the sequence (DNA module only)
Limit enzymes Limit enzymes so that only enzymes below a certain number of cuts in the sequence is shown (DNA module only)
PCR Compare DNA map
Selection Compare DNA map
Copy as image Copies the sequence map as a bitmap to the clipboard (Caveat : Such a bitmap can take up a huge amount of memory, depending on the length of the sequence)
Save as image Saves the sequence map in one of several image formats
Print sequence Prints the sequence

Keys[edit]

The whole sequence can be marked by Ctrl-A. The Find dialog can be invoked by Ctrl-F. Both functions can also be called upon through a menu.

In the DNA and PCR modules, the amino acid reading frame can be toggled by keys like this:

  • Ctrl-1 = reading frame 1
  • Ctrl-2 = reading frame 2
  • Ctrl-3 = reading frame 3
  • Ctrl-4 = reading frame 1, complementary strand
  • Ctrl-5 = reading frame 2, complementary strand
  • Ctrl-6 = reading frame 3, complementary strand
  • Ctrl-7 = all reading frames, one-letter code
  • Ctrl-8 = known reading frames only (from the features)
  • Ctrl-0 = hide amino acids
  • Ctrl-W = three-letter code (not when displaying all reading frames)
  • Ctrl-Q = one-letter code

Edit mode[edit]

Display and edit mode can be toggled by F2 or the toolbar. During editing, the sequence display is maximized, and the DNA map is hidden, improving ease of edit. Depending on the current module, only some keys are allowed (in the DNA module, "A", "C", "G", and "T") by default; any other key will trigger a request to allow all keys for that sequence, for that session. The cursor can be moved similar to that in a text editor. Insert and overwrite mode can be toggled, except for some modules like PCR or Sequencing, where overwrite mode is mandatory. In these modules, backspace and delete are diasbeled as well.

When editing a primer in PCR mode, the "." key copies the base at the current position from the 3'→5' or 5'→3' sequence, respectively.

Horizontal mode[edit]

In some modules, the sequence display can be toggled to horizontal. This can enhance visibility. Printing, however, is always done in standard ("vertical") mode.