The Assembly window

The assembly window consists in:

• the CONTIG MAP
• the ASSEMBLY GRID, this is where the assembled sequences and the consensus contig are displayed
• the CHROMATOGRAM VIEWER, 'were the corresponding chromatograms are displayed

The CONTING MAP, the ASSEMBLY GRID and the CHROMATOGRAM VIEWER are correlated, resulting in a synchronized display of the chromatograms, contig and contig map. This makes the correction of ambiguous bases much faster and easier.

Common used functions

Most functions related to this window are available in the main menu but some that often used are available via pop-up menu (right click on a sample to pop the menu) or right under the contig grid:

- Save changes to the contig and close the current window.

- See how the contig looks after it was saved to disk.

- Adjust the position of the bases relative to the peaks. It applies to the currently selected sample.

- Show/hide the contig map.

- Increase/decrease peak height. It applies to the currently selected sample.

Ambiguity navigation system

You can press the Next and Previous buttons to move the cursor to the next/previous ambiguity.

  - Navigate from ambiguous base to ambiguous base.

- Navigate from ambiguous base to ambiguous base.

Pressing the Next button will also mark the current ambiguity in green color to indicate that the user reviewed the ambiguity and accepted the base suggested by DNA Baser. If you don't want to automatically accept DNA Baser's suggestions, please keep the Control key depressed while clicking the Next button.

Colors in DNA Baser

In the ASSEMBLY GRID, the ambiguous bases are highlighted with the red color. The low quality bases in the untrusted regions removed by the Trimming Engine have a gray background. The recognition sequences used for vector removal are highlighted in light blue. The selection is yellow and the reference sequence is pink.

SNP analysis

DNA Baser does not offer SNP functionality per se. In case of SNP the base suggested by DNA Baser is not an IUPAC ambiguous base. However, DNA Baser highlights (see figure above) the ambiguities (SNP can be considered an ambiguity also) so you can use the Ambiguity Navigation System to navigate between SNP points.