skbio.sequence.GeneticCode.translate_six_frames¶
- GeneticCode.translate_six_frames(sequence, start='ignore', stop='ignore')[源代码]¶
用六种可能的阅读框架将RNA翻译成蛋白质。
状态:0.4.0稳定。
六种可能的阅读框架是:
1(前进)
2(前进)
3(向前)
-1(倒档)
-2(倒档)
-3(倒档)
翻译后的序列按此顺序产生。
- 参数:
sequence (RNA) -- 翻译RNA序列。
start ({'ignore', 'require', 'optional'}) -- 如何处理起始密码子。看到了吗
GeneticCode.translate
有关详细信息。stop ({'ignore', 'require', 'optional'}) -- 如何处理停止密码子。看到了吗
GeneticCode.translate
有关详细信息。
- 生成器:
蛋白质 --当前阅读帧中的翻译序列。
参见
备注
此方法比(相当于)执行六个独立的翻译要快,例如:
(gc.translate(seq, reading_frame=rf) for rf in GeneticCode.reading_frames)
输入的RNA序列元数据包含在每个翻译的蛋白质序列中。不包括位置元数据。
示例
使用六种可能的阅读框架和NCBI的标准遗传代码(表ID 1,scikit-bio中的默认遗传代码)将RNA转化为蛋白质:
>>> 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