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Ribbon multiple alignment and trace file edition

 
Ribbon multiple alignment and trace file edition
1

Edit button

1. Edit button
Options for editing the sequences, see Edit options.
 
2

More button

2. More button
More options. For details, see More options.
 
3

Align sequences and

optimize directions

3. Align sequences and optimize directions
- Align the selected sequence only.
- Align all sequences.
- Reverse the direction of the selected sequence.
4

Find conflicts

4. Find conflictsGo from the selected position to the previous or next conflict.
5

Find primers

5. Find primers
 
Saved primers can be selected and used to find the position of the primer in the sequence(s).
 
6

RC primer

6. RC primer
 
Activate this button to search for the reverse compliment primer sequence.
 
7

Find sequence

7. Find sequence
Search for a given part of the sequence.
 
8

Base caller

8. Base caller
This value is used to calculate the threshold level, depending on the selected algorithm in the Options dialog.
 
9

Zoom in/out

horizontally

9. Zoom in/out horizontally
Adapt the width of the peaks.
 
10

Zoom in/out

vertically

10. Zoom in/out vertically
Adapt the height of the peaks.
 
11

Higher/Smaller

11. Higher/Smaller
Enlarge the height of the sequence section.
 
12

Collapse/Expand

12. Collapse/Expand
Collapse or expand the sequence section (expand to see the waves).
 
13

Show or hide

chromatogram

13. Show or hide chromatogram
Show or hide chromatogram for each of the nucleotides.
 
14

Confidence

level

14. Confidence level
Show or hide the level of confidence of the consensus base pare at any given point of the alignment.
 
A confidence value can be computed for each nucleotide. The trace wave is giving the intensity of the signal for each of the four nucleotides.
15

Majority rule

display

15. Majority rule display
When checked this option will display the most frequent letter at any given point of the alignment.
 
16

Ambiguity

letters

16. Ambiguity letters
Letters displayed in the consensus sequence are ambiguity letters instead of majority rule letters.
 
17

Colored

background

17. Colored background
Letters will be displayed in black with colored background.
 
18

Show colored

letters

18. Show colored letters
Letters will be displayed in colors with a white background.
 
19

Regular

interval

19. Regular interval
When checked, this option makes the interval between base pairs regular or standardized. Otherwise the original trace file file is displayed.
 
20

Show

conflicts

20. Show conflicts
 
Check this button to see the conflicts between the basepairs. When unchecked, the protein letters are displayed (based on selected the Protein translation option).
 
21

Protein

translation

options

21. Protein translation options
 
Frames: 1, 2 or 3. Position of the 3 nucleotides being translated to protein. Shifting 1 position each frame.
 
Genetic code: DNA is translated to proteins using these genetic codes:
Choose from: Standard, Mitochondrial, Yeast Mitochondrial, Invertebrate, Ciliate Nuclear, Echinoderm Mitochondrial, Mycoplasma, Bacterial.
 
22

Redraw tree

22. Redraw tree
Select one of the nine provided algorithms to (re)draw a tree based on the sequences.
 
23

Toggle tree display

23. Toggle tree display
Removes the drawn tree in front of the multiple alignment.
 
 

The contents of Ribbon multiple alignment and trace file edition

Edit options
More options
(c) BioAware, 2024