Viewers for sequencing data files
Sequence Scanner v 1.0
Free viewing software provided by Applied Biosystems for Windows. The Sequence Scanner Software enables you to view, edit, print and export sequence data generated using Applied Biosystems genetic analyser instruments. Other features include:
- Graphical reports on results.
- View software assigned quality values.
- View simultaneously the analysed and raw trace data for a single trace.
- Spot sample failures readily with reports such as the Plate Report
- Export traces into commonly used presentation formats (.jpeg, .pdf)
Quality values
The 3130xl uses Applied Biosystems DNA Sequencing Analysis Software v 5.2 with KB Basecaller. The KB basecaller assigns quality values to each basecall (pure and mixed bases). The QV is calculated using the following equation: QV = -10log10(PE) where PE is the probability that a basecall is erroneous.
QV's range from 1 to 50+. The calculated QV for each base may be visualised on the analysed data as coloured QV bars above each basecall. These QV bars are only visible using the DNA Sequencing Analysis Software or Applied Biosystems SequenceScanner program (see Viewers for sequencing data files above).
IUPAC / IUB codes
The IUPAC / IUB Codes, defined by the International Union of Biochemistry, represent the occurrence of mixed bases at a given position in a sequence. The Sequencing Analysis Software v 5.2 uses these codes in place of Ns in the sequence data. The table below contains a list of the codes and the mixed bases they represent.
| BASE | IUB Code | Complement |
|---|---|---|
| Adenosine | A | T |
| Cytidine | C | G |
| Guanosine | G | C |
| Thymidine | T | A |
| Adenosine or Guanosine (purine) | R | Y |
| Cytidine or Thymidine (pYrimidine) | Y | R |
| Guanosine or Thymidine (Keto) | K | M |
| Adenosine or Cytidine (aMino) | M | K |
| Guanosine or Cytidine (Strong - 3 Hydrogen bonds) | S | S |
| Adenosine or Thymidine (Weak - 2 Hydrogen bonds) | W | W |
| Cytidine, Guanosine or Thymidine | B | V |
| Cytidine, Guanosine or Thymidine | D | H |
| Adenosine, Guanosine or Thymidine | H | D |
| Adenosine, Cytidine or Guanosine | V | B |
| Adenosine, Cytidine, Guanosine or Thymidine (aNy base) | N | N |