skbio.sequence.GeneticCode.translate_six_frames

GeneticCode.translate_six_frames(sequence, start='ignore', stop='ignore')

Translate RNA into protein using six possible reading frames.

The six possible reading frames are:

• 1 (forward)

• 2 (forward)

• 3 (forward)

• -1 (reverse)

• -2 (reverse)

• -3 (reverse)

Translated sequences are yielded in this order.

Parameters:

sequenceRNA

RNA sequence to translate.

start{‘ignore’, ‘require’, ‘optional’}

How to handle start codons. See GeneticCode.translate for details.

stop{‘ignore’, ‘require’, ‘optional’}

How to handle stop codons. See GeneticCode.translate for details.

Yields:

Protein

Translated sequence in the current reading frame.

See also

translate

Notes

This method is faster than (and equivalent to) performing six independent translations using, for example:

(gc.translate(seq, reading_frame=rf) for rf in GeneticCode.reading_frames)

Input RNA sequence metadata are included in each translated protein sequence. Positional metadata are not included.

Examples

Translate RNA into protein using the six possible reading frames and NCBI’s standard genetic code (table ID 1, the default genetic code in scikit-bio):

>>> from skbio import RNA, GeneticCode
>>> rna = RNA('AUGCCACUUUAA')
>>> sgc = GeneticCode.from_ncbi()
>>> for protein in sgc.translate_six_frames(rna):
...     protein
...     print('')
Protein
--------------------------
Stats:
    length: 4
    has gaps: False
    has degenerates: False
    has definites: True
    has stops: True
--------------------------
0 MPL*

Protein
--------------------------
Stats:
    length: 3
    has gaps: False
    has degenerates: False
    has definites: True
    has stops: False
--------------------------
0 CHF

Protein
--------------------------
Stats:
    length: 3
    has gaps: False
    has degenerates: False
    has definites: True
    has stops: False
--------------------------
0 ATL

Protein
--------------------------
Stats:
    length: 4
    has gaps: False
    has degenerates: False
    has definites: True
    has stops: False
--------------------------
0 LKWH

Protein
--------------------------
Stats:
    length: 3
    has gaps: False
    has degenerates: False
    has definites: True
    has stops: True
--------------------------
0 *SG

Protein
--------------------------
Stats:
    length: 3
    has gaps: False
    has degenerates: False
    has definites: True
    has stops: False
--------------------------
0 KVA