Multiple Sequence Alignment with Clustal Omega¶

PyEED provides a convenient interface to Clustal Omega for multiple sequence alignment. This notebook demonstrates how to:

1. Align sequences from a dictionary
2. Align sequences directly from the database

In [13]:

from pyeed import Pyeed
from pyeed.tools.clustalo import ClustalOmega

# change log level to INFO
import sys
from loguru import logger

logger.remove()
level = logger.add(sys.stderr, level="INFO")

from pyeed import Pyeed from pyeed.tools.clustalo import ClustalOmega # change log level to INFO import sys from loguru import logger logger.remove() level = logger.add(sys.stderr, level="INFO")

Direct Sequence Alignment¶

You can align sequences directly by providing a dictionary of sequences:

In [14]:

# Initialize ClustalOmega
clustalo = ClustalOmega()

# Example sequences
sequences = {
    "seq1": "AKFVMPDRAWHLYTGNECSKQRLYVWFHDGAPILKTQSDNMGAYRCPLFHVTKNWEI",
    "seq2": "AKFVMPDRQWHLYTGQECSKQRLYVWFHDGAPILKTQSDNMGAYRCPLFHVTKNWEI",
    "seq3": "AKFVMPDRQWHLYTGNECSKQRLYVWFHDGAPILKTQADNMGAYRCALFHVTK",
}

# Perform alignment
alignment = clustalo.align(sequences)
print("Aligned sequences:")
print(alignment)

# Initialize ClustalOmega clustalo = ClustalOmega() # Example sequences sequences = { "seq1": "AKFVMPDRAWHLYTGNECSKQRLYVWFHDGAPILKTQSDNMGAYRCPLFHVTKNWEI", "seq2": "AKFVMPDRQWHLYTGQECSKQRLYVWFHDGAPILKTQSDNMGAYRCPLFHVTKNWEI", "seq3": "AKFVMPDRQWHLYTGNECSKQRLYVWFHDGAPILKTQADNMGAYRCALFHVTK", } # Perform alignment alignment = clustalo.align(sequences) print("Aligned sequences:") print(alignment)

Aligned sequences:
seq1  AKFVMPDRAWHLYTGNECSKQRLYVWFHDGAPILKTQSDNMGAYRCPLFHVTKNWEI
seq2  AKFVMPDRQWHLYTGQECSKQRLYVWFHDGAPILKTQSDNMGAYRCPLFHVTKNWEI
seq3  AKFVMPDRQWHLYTGNECSKQRLYVWFHDGAPILKTQADNMGAYRCALFHVTK----

Database-based Alignment¶

You can also align sequences directly from the database by providing a list of accession IDs:

In [15]:

# Connect to database
pyeed = Pyeed(uri="bolt://129.69.129.130:7687", user="neo4j", password="12345678")

# Get protein IDs from database
from pyeed.model import Protein

accession_ids = [protein.accession_id for protein in Protein.nodes.all()][:10]

# Align sequences from database
alignment = clustalo.align_from_db(accession_ids, pyeed.db)
print("Database alignment:")
print(alignment)

# Connect to database pyeed = Pyeed(uri="bolt://129.69.129.130:7687", user="neo4j", password="12345678") # Get protein IDs from database from pyeed.model import Protein accession_ids = [protein.accession_id for protein in Protein.nodes.all()][:10] # Align sequences from database alignment = clustalo.align_from_db(accession_ids, pyeed.db) print("Database alignment:") print(alignment)

Pyeed Graph Object Mapping constraints not defined. Use _install_labels() to set up model constraints.
📡 Connected to database.
Database alignment:
AAP20891.1      MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW
CAJ85677.1      MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW
SAQ02853.1      MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW
CDR98216.1      MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW
WP_109963600.1  MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGTGKRGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW
CAA41038.1      MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW
WP_109874025.1  MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW
CAA46344.1      MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGASERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW
APG33178.1      MSIQHFRVALIPFFAAFCFPVFAHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVKYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDSWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYMTGSQATMDERNRQIAEIGASLIKHW
AKC98298.1      MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDKLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRVDAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRLDHWEPELNEAIPNDERDTTMPAAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPLLRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGASLIKHW

Understanding Alignment Results¶

The alignment result is a MultipleSequenceAlignment object with:

• List of Sequence objects
• Each sequence has an ID and aligned sequence
• Gaps are represented by '-' characters
• Sequences are padded to equal length

The alignment preserves sequence order and maintains sequence IDs from the input.

Configuration¶

ClustalOmega requires the PyEED Docker service to be running. Make sure to:

1. Have Docker installed
2. Start the service with docker-compose up -d
3. The service runs on port 5001 by default