Align sequences¶

In [5]:

import json
from pyeed.core import ProteinRecord


# load accession ids from json file
with open("ids.json", "r") as f:
    ids = json.load(f)

sequences = ProteinRecord.get_ids(ids)

import json from pyeed.core import ProteinRecord # load accession ids from json file with open("ids.json", "r") as f: ids = json.load(f) sequences = ProteinRecord.get_ids(ids)

Output()

Multi Sequence Alignment¶

A multi sequence alignment can be calculated by creating a MSA object and passing a list of ProteinRecord. The alignment can be executed by calling the clustalo method. In order for the clustalo method to work, the PyEED Docker Service must be running. The clustalo method will return an AlignmentResult containing all input sequences and aligned_sequences.

In [10]:

from pyeed.align import MSA

alignment = MSA(sequences=sequences).clustalo()
alignment.visualize()

from pyeed.align import MSA alignment = MSA(sequences=sequences).clustalo() alignment.visualize()

Output()

✅ Alignment completed

Create a HMM profile¶

To create a hidden markov model profile, you can use the HMM class. This method receives a MSA object to create the model. To check if a sequence belongs to the profile, you can use the search method. This method takes a ProteinRecord object and returns a HMMResult object containing the sequence and the score of the sequence in the profile.

In [3]:

from pyeed.align import HMM

model = HMM(name="random profile", alignment=alignment)
hits = model.search(sequence=sequences[0])

from pyeed.align import HMM model = HMM(name="random profile", alignment=alignment) hits = model.search(sequence=sequences[0])

In [9]:

alignment.sequences[0]

alignment.sequences[0]

Out[9]:

Sequence(id='85d6e902-3cb0-44f2-947f-54c2a0f220e1', sequence_id='C3MJ04', sequence='MRNINVQLNPLSDIEKLQVELVERKGLGHPDYIADAVAEEASRKLSLYYLKKYGVILHHNLDKTLVVGGQATPRFKGGDVIQPIYIVVAGRATTEVKTESGIEQIPVGTIIIESVKEWIRNNFRYLDAEKHLIVDYKIGKGSTDLVGIFEAGKRVPLSNDTSFGVGFAPFTKLEKLVYETERHLNSKQFKAKLPEVGEDIKVMGLRRGNEVDLTIAMATISELIEDVNHYINVKEQAKNEILDLASKIAPDYDVRIYVNTGDKIDKNILYLTVTGTSAEHGDDGMTGRGNRGVGLITPMRPMSLEATAGKNPVNHVGKLYNVLANLIANKIAQEVKDVKFSQVQVLGQIGRPIDDPLIANVDVITYDGKLNDETKNEISGIVDEMLSSFNKLTELILEGKATLF', json_ld_type=['Sequence'], json_ld_context={'Sequence': 'https://github.com/PyEED/pyeed/Sequence'})

In [ ]: