from cogent3 import get_app
loader = get_app("load_unaligned", format_name="fasta")
to_aa = get_app("translate_seqs")
process = loader + to_aa
seqs = process("data/SCA1-cds.fasta")Using a protein model
We use apps to load unaligned DNA sequences and to translate them into amino acids.
Protein alignment with default settings
The default setting for “protein” is a WG01 model.
from cogent3 import get_app
aa_aligner = get_app("progressive_align", "protein")
aligned = aa_aligner(seqs)
aligned| 0 | |
| Human | MKSNQERSNECLPPKKREIPATSRSSEEKAPTLPSDNHRVEGTAWLPGNPGGRGHGGGRH |
| Chimp | ............................................................ |
| Mouse Lemur | ...............................A.......A..AP................ |
| Rat | ........................P.....TA......C...V....ST..S........ |
| Mouse | ........................P.....TA......C...V....ST..I........ |
| Macaque | ........................P......A............................ |
6 x 825 (truncated to 6 x 60) protein alignment
Specify a different distance measure for estimating the guide tree
The distance measures available are percent or paralinear.
Note
An estimated guide tree has its branch lengths scaled so they are consistent with usage in a codon model.
aa_aligner = get_app("progressive_align", "protein", distance="paralinear")
aligned = aa_aligner(seqs)
aligned| 0 | |
| Human | MKSNQERSNECLPPKKREIPATSRSSEEKAPTLPSDNHRVEGTAWLPGNPGGRGHGGGRH |
| Rat | ........................P.....TA......C...V....ST..S........ |
| Mouse | ........................P.....TA......C...V....ST..I........ |
| Mouse Lemur | ...............................A.......A..AP................ |
| Macaque | ........................P......A............................ |
| Chimp | ............................................................ |
6 x 825 (truncated to 6 x 60) protein alignment
Alignment settings provenance
The parameters used to construct the alignment, including the guide tree and substitution model, are record in the alignment info attribute.
aligned.info{'Refs': {},
'align_params': {'indel_length': 0.1,
'indel_rate': 1e-10,
'guide_tree': '((((Rat:0.004763355238688913,Mouse:0.011219581285708921):0.052856143725369786,Mouse_Lemur:0.03580862702845759):0.024351474041303382,Macaque:0.0023127545121458537):0.003074310394311757,(Chimp:0.008168683695808834,Human:0.0001974014915215993):1e-06);',
'model': 'JTT92',
'lnL': -3199.438263579326}}The file from which the alignment was derived (the provenance) is on the .source attribute.
aligned.source'SCA1-cds'