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sequence assembly

Contig Assembly window

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The assembly window consists from 3 parts:

 

- the CONTIG MAP
- the CONTIG GRID (the middle part of the picture below), this is were the assembled sequences and the consensus contig are displayed
- the CHROMATOGRAM VIEWER, 'were the corresponding chromatograms are displayed

 

The CONTING MAP, the CONTIG 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.

 

contig assembly window with chromatogram viewer and contig map

 

ambigous bases  - use this button to navigate from ambiguous base to ambiguous base.

previous button - use this button to navigate from ambiguous base to ambiguous base.

save contig - use this button to save changes to the contig

view contig button - use this button to see the contig how it is saved on disk

trace srool - use this to scroll the selected chromatogram

DNA chromatogram height - use this trackbar (in the selected chromatograms) to move the position of the bases relative to the peaks

chromatogram - show / hide the trackbar for the peak height

contig map button - show / hide the contig map

chromatogram height - use this trackbar to increase/decrease peak height in the selected chromatogram

 

 

 

Colors in DNA Baser

 

In the CONTIG GRID, the ambiguous bases are highlighted with the red color.
The bases removed following end trimming have a gray background. The recognition sequences used for vector removal are highlighted in light blue:

 

 

 

Automatic trimming engine


DNA Baser is removing automatically the low quality ends from the chromatograms before starting the assembly process. Please see details about this important process here.


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DNA sequence assembly