AAindex.AMatrix — Type

An amino acid mutation and contact potential matrix is generally 20 × 20 numerical values representing similarity of amino acids.

Note that the row/column identities may not represent standard amino acid labels depending on the source paper. They should be interpreted by the user.

Each entry has the following format:

  • H Accession number
  • D Data description
  • R PMID
  • A Author
  • T Title of the article
  • J Journal reference
    • Comment or missing
  • M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV AA AR RR AN RN NN AD RD ND DD AC RC NC DC CC AQ RQ NQ DQ CQ QQ AE RE NE DE CE QE EE AG RG NG DG CG QG EG GG AH RH NH DH CH QH EH GH HH AI RI NI DI CI QI EI GI HI II AL RL NL DL CL QL EL GL HL IL LL AK RK NK DK CK QK EK GK HK IK LK KK AM RM NM DM CM QM EM GM HM IM LM KM MM AF RF NF DF CF QF EF GF HF IF LF KF MF FF AP RP NP DP CP QP EP GP HP IP LP KP MP FP PP AS RS NS DS CS QS ES GS HS IS LS KS MS FS PS SS AT RT NT DT CT QT ET GT HT IT LT KT MT FT PT ST TT AW RW NW DW CW QW EW GW HW IW LW KW MW FW PW SW TW WW AY RY NY DY CY QY EY GY HY IY LY KY MY FY PY SY TY WY YY AV RV NV DV CV QV EV GV HV IV LV KV MV FV PV SV TV WV YV VV
AAindex.Index — Type

An amino acid index is a set of 20 numerical values representing various physico-chemical and biochemical properties of amino acids.

AAindex.Metadata — Type

Each entry has the following format:

  • H Accession number
  • D Data description
  • R PMID
  • A Author(s)
  • T Title of the article
  • J Journal reference
    • Comment or missing
  • C Accession numbers of similar entries with the correlation coefficients of 0.8 (-0.8) or more (less). Notice: The correlation coefficient is calculated with zeros filled for missing values.
  • I Amino acid index data in the following order Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val
AAindex.is_key — Method
is_key(candidate)

Checks if provided candidate key matches the format for AAindex accession numbers.

AAindex.parse — Function
parse(path, [targets])

Reads and parses the AAindex file located at path. Optionally, specific entry IDs (denoted by H) can be provided in targets.

AAindex.search — Function
search(term, [aaindex_directory])

Performs a naive substring search for provided term in the key and title fields of records in the database. Returns an unsorted list of entries containing the term.

AAindex.search_id — Function
search_id(key, [aaindex_directory])

Searches for specified AAindex entry key (accession number) and returns the loaded entry. Throws an error if the key is not in the database.