mkt.databases.aligners

Pairwise and multiple-sequence aligner wrappers for mapping kinase sequences onto UniProt.

Wraps Clustal Omega (ClustalOmegaAligner) and Biopython (BioAligner) behind a common CustomAligner interface, with specializations for aligning BLOSUM-based and KinCore sequences to UniProt.

Classes

`BL2UniProtAligner`([substitution_matrix, ...])
`BioAligner`([substitution_matrix, mode, ...])	BioPython aligner class for aligning sequences.
`ClustalOmegaAligner`(list_sequences[, ...])	ClustalOmega aligner class for multiple sequence alignments (need to initialize with list of sequences).
`CustomAligner`()	Custom aligner class for aligning sequences.
`Kincore2UniProtAligner`([...])

class mkt.databases.aligners.BL2UniProtAligner(substitution_matrix: str = 'BLOSUM90', mode: str = 'global', gap_score: int = -5, extend_gap_score: int = -1)[source]

Bases: BioAligner

__init__(substitution_matrix: str = 'BLOSUM90', mode: str = 'global', gap_score: int = -5, extend_gap_score: int = -1) → None

mode: str = 'global'

Alignment mode. Default is “global.

Type:: str

class mkt.databases.aligners.BioAligner(substitution_matrix: str = 'BLOSUM90', mode: str = 'local', gap_score: int = -5, extend_gap_score: int = -1)[source]

Bases: CustomAligner

BioPython aligner class for aligning sequences. Initialized without sequences

Align = <module 'Bio.Align' from '/home/docs/checkouts/readthedocs.org/user_builds/missense-kinase-toolkit/conda/latest/lib/python3.10/site-packages/Bio/Align/__init__.py'>

__init__(substitution_matrix: str = 'BLOSUM90', mode: str = 'local', gap_score: int = -5, extend_gap_score: int = -1) → None

align(seq1: str, seq2: str) → MultipleSeqAlignment[source]: Abstract method for aligning sequences.

extend_gap_score: int = -1

Gap extension score. Default is -1.

Type:: int

gap_score: int = -5

Gap score. Default is -5.

Type:: int

mode: str = 'local'

Alignment mode. Default is “local”.

Type:: str

substitution_matrix: str = 'BLOSUM90'

Substitution matrix used. Default is BLOSUM90 to maximize mismatch penalty.

Type:: str

class mkt.databases.aligners.ClustalOmegaAligner(list_sequences: list[str], substitution_matrix: str = 'BLOSUM62', path_bin: str = '/usr/local/bin/clustalo')[source]

Bases: CustomAligner

ClustalOmega aligner class for multiple sequence alignments (need to initialize with list of sequences).

__init__(list_sequences: list[str], substitution_matrix: str = 'BLOSUM62', path_bin: str = '/usr/local/bin/clustalo') → None

align() → str[source]: Abstract method for aligning sequences.

list_sequences: list[str]

List of sequences to align.

Type:: list[str]

path_bin: str = '/usr/local/bin/clustalo'

Path to clustalo binary. Default is “/usr/local/bin/clustalo”.

Type:: str

substitution_matrix: str = 'BLOSUM62'

Substitution matrix used. Default is BLOSUM62.

Type:: str

class mkt.databases.aligners.CustomAligner[source]

Bases: ABC

Custom aligner class for aligning sequences.

abstract align(*args, **kwargs)[source]: Abstract method for aligning sequences.

class mkt.databases.aligners.Kincore2UniProtAligner(substitution_matrix: str = 'BLOSUM90', mode: str = 'local', gap_score: int = -5, extend_gap_score: int = -1)[source]

Bases: BioAligner

__init__(substitution_matrix: str = 'BLOSUM90', mode: str = 'local', gap_score: int = -5, extend_gap_score: int = -1) → None

mode: str = 'local'

Alignment mode. Default is “local.

Type:: str