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Last update on 25. Nov 2018 .
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Protein Viewer

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.
Refer to ´Translation tables´ for details.

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