GENtle/Sequencing

From Wikibooks, open books for an open world
< GENtle
Jump to: navigation, search
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 sequencing module

The sequencing module allows to view the data recorded by a sequence analyser. The data is loaded by importing the appropriate .abi/.ab1 file.

Display[edit]

The data is displayed in the main sequence window. The text window on the upper right shows data stored in the file. On the left side, the following display options for the sequence are available:

Help lines Gray vertial lines down from each sequence letter to the baseline. These can help to identify which letter belongs to which peak
Invert&complement Shows the sequencing complement/inverted. Useful for Alignments
Scale height Sets the height of the graphic display [unit in text lines]
Scale width Sets the graphical points per data value. Default is 2; 1 would mean one pixel width per data point
Zoom Sets the zoom factor for the data; useful to see small peaks

Toolbar[edit]

  • Enter new sequence
  • Open sequence
  • Save sequence (see caveats)
  • Copy sequence to clipboard
  • Horizontal mode

Caveats[edit]

  • Editing works in overwrite-mode only
  • Saving will only store the sequence in the database, not the sequencer data (the peaks), due to memory concerns.