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# Copyright 2004 by Iddo Friedberg.
# All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Reduced alphabets which lump together several amino-acids into one letter.
Reduced (redundant or simplified) alphabets are used to represent protein
sequences using an alternative alphabet which lumps together several
amino-acids into one letter, based on physico-chemical traits. For example,
all the aliphatics (I,L,V) are usually quite interchangeable, so many sequence
studies group them into one letter
Examples of reduced alphabets are available in:
http://viscose.herokuapp.com/html/alphabets.html
The Murphy tables are from here:
Murphy L.R., Wallqvist A, Levy RM. (2000) Simplified amino acid
alphabets for protein fold recognition and implications for folding.
Protein Eng. 13(3):149-152
These alphabets have been used with Bio.utils.reduce_sequence, which has been
removed from Biopython. You can use this is alphabets and tables like this:
>>> from Bio.Seq import Seq
>>> from Bio import Alphabet
>>> from Bio.Alphabet import Reduced
>>> my_protein = Seq('MAGSKEWKRFCELTINEA', Alphabet.ProteinAlphabet())
Now, we convert this sequence into a sequence which only recognizes polar (P)
or hydrophobic (H) residues:
>>> new_protein = Seq('', Alphabet.Reduced.HPModel())
>>> for aa in my_protein:
... new_protein += Alphabet.Reduced.hp_model_tab[aa]
>>> new_protein
Seq('HPPPPPHPPHHPHPHPPP', HPModel())
The following Alphabet classes are available:
- Murphy15: Maps 20 amino acids to 15, use murphy_15_tab for conversion,
ambiguous letters: L: LVIM, F: FY, K: KR
- Murphy10: Maps 20 amino acids to 10, use murphy_10_tab for conversion,
ambiguous letters: L: LVIM, S: ST, F: FYW, E: EDNQ, K: KR
- Murphy8: Maps 20 amino acids to 8, use murphy_8_tab for conversion,
ambiguous letters: L: LVIMC, A: AG, S: ST, F: FYW, E: EDNQ,
K: KR
- Murphy4: Maps 20 amino acids to 4, use murphy_4_tab for conversion,
ambiguous letters: L: LVIMC, A: AGSTP, F: FYW, E: EDNQKRH
- HPModel: Groups amino acids as polar (hydrophilic) or hydrophobic
(non-polar), use hp_model_tab for conversion,
P: AGTSNQDEHRKP, H: CMFILVWY
- PC5: Amino acids grouped according to 5 physico-chemical properties,
use pc_5_table for conversion,
A (Aliphatic): IVL, R (aRomatic): FYWH, C (Charged): KRDE, T (Tiny):
GACS, D (Diverse): TMQNP
"""
from Bio import Alphabet
murphy_15_tab = {"L": "L",
"V": "L",
"I": "L",
"M": "L",
"C": "C",
"A": "A",
"G": "G",
"S": "S",
"T": "T",
"P": "P",
"F": "F",
"Y": "F",
"W": "W",
"E": "E",
"D": "D",
"N": "N",
"Q": "Q",
"K": "K",
"R": "K",
"H": "H"}
class Murphy15(Alphabet.ProteinAlphabet):
"""Reduced protein alphabet with 15 letters.
Letters: A, C, D, E, G, H, N, P, Q, S, T, W,
L(LVIM), F(FY), K(KR)
"""
letters = "LCAGSTPFWEDNQKH"
size = 1
murphy_15 = Murphy15()
murphy_10_tab = {"L": "L",
"V": "L",
"I": "L",
"M": "L",
"C": "C",
"A": "A",
"G": "G",
"S": "S",
"T": "S",
"P": "P",
"F": "F",
"Y": "F",
"W": "F",
"E": "E",
"D": "E",
"N": "E",
"Q": "E",
"K": "K",
"R": "K",
"H": "H"}
class Murphy10(Alphabet.ProteinAlphabet):
"""Reduced protein alphabet with 10 letters.
Letters: A, C, G, H, P, L(LVIM), S(ST), F(FYW),
E(EDNQ), K(KR)
"""
letters = "LCAGSPFEKH"
size = 1
murphy_10 = Murphy10()
murphy_8_tab = {"L": "L",
"V": "L",
"I": "L",
"M": "L",
"C": "L",
"A": "A",
"G": "A",
"S": "S",
"T": "S",
"P": "P",
"F": "F",
"Y": "F",
"W": "F",
"E": "E",
"D": "E",
"N": "E",
"Q": "E",
"K": "K",
"R": "K",
"H": "H"}
class Murphy8(Alphabet.ProteinAlphabet):
"""Reduced protein alphabet with 8 letters.
Letters: H, P, L(LVIMC), A(AG), S(ST), F(FYW),
E(EDNQ), K(KR)
"""
letters = "LASPFEKH"
size = 1
murphy_8 = Murphy8()
murphy_4_tab = {"L": "L",
"V": "L",
"I": "L",
"M": "L",
"C": "L",
"A": "A",
"G": "A",
"S": "A",
"T": "A",
"P": "A",
"F": "F",
"Y": "F",
"W": "F",
"E": "E",
"D": "E",
"N": "E",
"Q": "E",
"K": "E",
"R": "E",
"H": "E"}
class Murphy4(Alphabet.ProteinAlphabet):
"""Reduced protein alphabet with 4 letters.
Letters: L(LVIMC), A(AGSTP), F(FYW), E(EDNQKRH)
"""
letters = "LAFE"
size = 1
murphy_4 = Murphy4()
hp_model_tab = {"A": "P", # Hydrophilic
"G": "P",
"T": "P",
"S": "P",
"N": "P",
"Q": "P",
"D": "P",
"E": "P",
"H": "P",
"R": "P",
"K": "P",
"P": "P",
"C": "H", # Hydrophobic
"M": "H",
"F": "H",
"I": "H",
"L": "H",
"V": "H",
"W": "H",
"Y": "H"}
class HPModel(Alphabet.ProteinAlphabet):
"""Reduced protein alphabet with only two letters for polar or hydophobic.
Letters: P (polar: AGTSNQDEHRKP), H (hydrophobic: CMFILVWY)
"""
letters = "HP"
size = 1
hp_model = HPModel()
pc_5_table = {"I": "A", # Aliphatic
"V": "A",
"L": "A",
"F": "R", # Aromatic
"Y": "R",
"W": "R",
"H": "R",
"K": "C", # Charged
"R": "C",
"D": "C",
"E": "C",
"G": "T", # Tiny
"A": "T",
"C": "T",
"S": "T",
"T": "D", # Diverse
"M": "D",
"Q": "D",
"N": "D",
"P": "D"}
class PC5(Alphabet.ProteinAlphabet):
"""Reduced protein alphabet with 5 letters for physico-chemical properties.
Letters: A (Aliphatic: IVL), R (aRomatic: FYWH), C (Charged: KRDE),
T (Tiny: GACS), D (Diverse: TMQNP)
"""
letters = "ARCTD"
size = 1
pc5 = PC5()
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