Sequence Translation
To translate DNA alignment to amino acid:
segul sequence translate -d [path-to-alignment-files] -f [sequence-format-keyword]
The app will default to the standard code table (NCBI Table 1). Use the --table
option to set the translation table. For example, to translate DNA sequences using NCBI Table 2 (vertebrate MtDNA):
segul sequence translate -d loci/ -f fasta --table 2
You can also set the reading frame using the --rf
option:
segul sequence translate -d loci/ -f fasta --table 2 --rf 2
To show all the table options, use the --show-tables
flag:
segul sequence translate --show-tables
Supported Translation Tables
Table No | Genetic Code |
---|---|
1 | The Standard Code |
2 | The Vertebrate Mitochondrial Code |
3 | The Yeast Mitochondrial Code |
4 | The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code |
5 | The Invertebrate Mitochondrial Code |
6 | The Ciliate, Dasycladacean and Hexamita Nuclear Code |
9 | The Echinoderm and Flatworm Mitochondrial Code |
10 | The Euplotid Nuclear Code |
11 | The Bacterial, Archaeal and Plant Plastid Code |
12 | The Alternative Yeast Nuclear Code |
13 | The Ascidian Mitochondrial Code |
14 | The Alternative Flatworm Mitochondrial Code |
16 | Chlorophycean Mitochondrial Code |
21 | Trematode Mitochondrial Code |
22 | Scenedesmus obliquus Mitochondrial Code |
23 | Thraustochytrium Mitochondrial Code |
24 | Rhabdopleuridae Mitochondrial Code |
25 | Candidate Division SR1 and Gracilibacteria Code |
26 | Pachysolen tannophilus Nuclear Code |
29 | Mesodinium Nuclear Code |
30 | Peritrich Nuclear Code |
33 | Cephalodiscidae Mitochondrial UAA-Tyr Code |
Sources: NCBI Genetic Code Tables