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# Protein Viewer

- OCCURRENCE
- DESCRIPTION
- NOTES
- EXAMPLES
- WARNINGS
- BUGS

## OCCURRENCE

### ARB_EDIT4/View/Protein Viewer

## DESCRIPTION

### Use this function to display AminoAcid sequence along with the DNA sequence.

### There are six possible reading frames in every sequence, three starting at positions 1, 2 and 3 and going in 5'---->3' direction of a given sequence, and another three starting at positions 1, 2, and 3 and going in 5'--->3' direction of a given sequence of the complementary sequence.

### CODON TABLE:

Select the desired codon table from the list of standard codon tables normally used in translating protein genes.

### START POSITION:

Select the start position where the translation should begin at (base position). eg., 1, 2 or 3.

### STRAND TYPE:

Check the "Forward Strand" to use the given sequence (as displayed) for translation. And checking "Complementary Strand" uses complementary sequence of the displayed sequence for translation.

### By checking "Translate from database fields" , ProteinViewer extracts "translation/codon table" and "start position" from the database and uses the same for translation.

### By default, the translated (aminoacid) sequence will be displayed as single letter codes. eg., A for Arginine, etc., But you can disply three letter aminoacid code (eg., Met for methionine) in the translated sequence by checking "Display Aminoacid names" checkbox.

### Display options "text" and "box" will display aminoacid codes or colored boxes in the translated sequence, respectively.

### Display at "Marked", "Selected", "Cursor" and "All" will toggle the display of aminoacid sequence only for marked, selected, cursor position and all species in the editor, respectively.

### SAVE AMINOACID SEQUENCE ALIGNMENT:

Once the alignment is refined according to the aminoacid sequence, you can save the translated (aminoacid) sequence to the database as a new alignment.

## NOTES

### This function is only visible if you are editing an DNA alignment

## EXAMPLES

### None

## WARNINGS

### None

## BUGS

### No bugs known