:>"^(@sdZddlmZddddddddddddd d d d d d d d d d dd ddddddddddddddddiZGdddejZeZddddddddddddd d d d d d d d d d dd dd ddddddddddddddiZGdddejZeZ ddddddddddddd dd d d d d d d d dd dd ddddddddddddddiZ GdddejZ e Z ddddddddddddd dd dd dd dd d dd dd ddddddddddddddiZ GdddejZeZdd d d d d d d dd dd dd dd dd dd dd d d ddddd dddddddddddiZGdd d ejZeZddddddd dddddddddddddddd d dd dd d d d dddddddd diZGd!d"d"ejZeZd#S)$aC 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 )AlphabetLVIMCAGSTPFYWEDNQKRHc@s"eZdZdZdZdZdS)Murphy15zReduced protein alphabet with 15 letters. Letters: A, C, D, E, G, H, N, P, Q, S, T, W, L(LVIM), F(FY), K(KR) ZLCAGSTPFWEDNQKHN)__name__ __module__ __qualname____doc__letterssizerr9/tmp/pip-build-ww9dw3qa/biopython/Bio/Alphabet/Reduced.pyrXs rc@s"eZdZdZdZdZdS)Murphy10zReduced protein alphabet with 10 letters. Letters: A, C, G, H, P, L(LVIM), S(ST), F(FYW), E(EDNQ), K(KR) Z LCAGSPFEKHrN)rrrrrrrrrr r!{s r!c@s"eZdZdZdZdZdS)Murphy8z}Reduced protein alphabet with 8 letters. Letters: H, P, L(LVIMC), A(AG), S(ST), F(FYW), E(EDNQ), K(KR) ZLASPFEKHrN)rrrrrrrrrr r"s r"c@s"eZdZdZdZdZdS)Murphy4zbReduced protein alphabet with 4 letters. Letters: L(LVIMC), A(AGSTP), F(FYW), E(EDNQKRH) ZLAFErN)rrrrrrrrrr r#s r#c@s"eZdZdZdZdZdS)HPModelzReduced protein alphabet with only two letters for polar or hydophobic. Letters: P (polar: AGTSNQDEHRKP), H (hydrophobic: CMFILVWY) ZHPrN)rrrrrrrrrr r$s r$c@s"eZdZdZdZdZdS)PC5zReduced protein alphabet with 5 letters for physico-chemical properties. Letters: A (Aliphatic: IVL), R (aRomatic: FYWH), C (Charged: KRDE), T (Tiny: GACS), D (Diverse: TMQNP) ZARCTDrN)rrrrrrrrrr r%s r%N)rZBiorZ murphy_15_tabZProteinAlphabetrZ murphy_15Z murphy_10_tabr!Z murphy_10Z murphy_8_tabr"Zmurphy_8Z murphy_4_tabr#Zmurphy_4Z hp_model_tabr$Zhp_modelZ pc_5_tabler%Zpc5rrrr =s