| More docs on the ARB website. See also index of helppages. Last update on 27. Jun 2017 .

Main topics:

- ARB: a Short Introduction
- Glossary

Related topics:

- Realign DNA
- Extract genes to gene-species

# Translate DNA to Protein

- OCCURRENCE
- DESCRIPTION
- AUTOMATIC SELECTION OF TRANSLATION PARAMETERS
- MANUAL SELECTION OF TRANSLATION PARAMETERS
- OTHER OPTIONS
- WARNINGS
- NOTES
- BUGS

## OCCURRENCE

### ARB_NT/Sequence/Translate

## DESCRIPTION

### Translates nucleic acid sequences. The alignment of the amino acid sequences is adapted to that of the nucleic acids. The one letter code is used.

## AUTOMATIC SELECTION OF TRANSLATION PARAMETERS

### To allow easy translation of gene sequences you may select to use two entries of the species:

- codon_start, which has to be 1, 2 or 3
- transl_table, which has to be a valid genetic code number. Refer to the numbers in the codon table selector to determine which genetic codes are known by ARB. These numbers are the same as the translation table numbers used in the EMBL database.

### These 2 fields are extracted from genes to gene-species automatically (see ´Extract genes to gene-species´).

### If both fields are missing, the selected values for 'Start position' and 'Codon table' are used. If one field is missing an error is raised.

## MANUAL SELECTION OF TRANSLATION PARAMETERS

1. Select source and destination alignment from the respective subwindows.
2. Select reading frame by pressing the 'Start position' button and selecting first, second or third absolute position. Alternatively you can position the cursor in ARB_EDIT4 at start of the reading frame.
3. Select the codon table to use.
4. Press the 'TRANSLATE' button. All marked sequences will be translated.
   Example:

       DNA:    ---UGG...GUAUGGUUA
       PRO:    -Y.LYG

## OTHER OPTIONS

### By checking the 'Save settings' toggle, the used values for the start position and the translation table are written into the corresponding fields ('codon_start' and 'transl_table') of every "translated species". That happens in Manual and Automatic mode.

### By checking the 'Translate all data' button, the translation insert a 'X' in front of the generated amino acid sequence, if you select starting position 2 or 3 and if there are nucleotides in front of that starting position. Later automatic realignments would fail if that 'X' is missing!

## WARNINGS

### The program does NOT begin at the first three bases, but at the first three alignment positions. That means that all your three letter codons should start at every third position.

    Example:        (### codon for aminoacid # )

    DNA:            ...111...222...333444
    PRO:            .1.2.34

    DNA:            ..111...222....333444
    PRO:            XXXX.34     // 1 2 are out of sync

    DNA:            ...111...22.2..333444
    PRO:            .1.XX34         // bad alignment for 2

## NOTES

### 'Mold/Protozoan/Coelenterate Mitochondrial Code' and 'Mycoplasma/Spiroplasma Code' are identical (Genetic code 4). For that reason the latter has been removed.

## BUGS

### If the editor is opened the reading frame changes after translation.