AAindex.jl

A package to read AAindex database files. These contain a variety of reported physico-chemical and biochemical properties of amino acids (Kawashima and Kanehisa, 2000). The package now also provides a copy of the database files (v9.2) for convenience. However, you may still use your own copy if you want to.

Usage

The main interface provided by this package is the search function, which accepts a search term (e.g., ANDN920101 or hydrophobicity) and, optionally, a path to an AAindex database file. It will search through the database and return a list of matching database entries. Additionally, the search_id function provides a more direct interface for loading a specific entry.

julia> search("hydrophobicity")
16-element Vector{Tuple{String, String, DataType}}:
 ("CIDH920103", "Normalized hydrophobicity scales for alpha+beta-proteins (Cid et al., 1992)", Index)
 ("CIDH920102", "Normalized hydrophobicity scales for beta-proteins (Cid et al., 1992)", Index)
 ("CIDH920105", "Normalized average hydrophobicity scales (Cid et al., 1992)", Index)
 ("EISD840101", "Consensus normalized hydrophobicity scale (Eisenberg, 1984)", Index)
 ("JURD980101", "Modified Kyte-Doolittle hydrophobicity scale (Juretic et al., 1998)", Index)
 ("BLAS910101", "Scaled side chain hydrophobicity values (Black-Mould, 1991)", Index)
 ("PONP800106", "Surrounding hydrophobicity in turn (Ponnuswamy et al., 1980)", Index)
 ("CIDH920104", "Normalized hydrophobicity scales for alpha/beta-proteins (Cid et al., 1992)", Index)
 ("SWER830101", "Optimal matching hydrophobicity (Sweet-Eisenberg, 1983)", Index)
 ("PONP800101", "Surrounding hydrophobicity in folded form (Ponnuswamy et al., 1980)", Index)
 ("CIDH920101", "Normalized hydrophobicity scales for alpha-proteins (Cid et al., 1992)", Index)
 ("MANP780101", "Average surrounding hydrophobicity (Manavalan-Ponnuswamy, 1978)", Index)
 ("PONP800103", "Average gain ratio in surrounding hydrophobicity (Ponnuswamy et al., 1980)", Index)
 ("PONP800105", "Surrounding hydrophobicity in beta-sheet (Ponnuswamy et al., 1980)", Index)
 ("PONP800102", "Average gain in surrounding hydrophobicity (Ponnuswamy et al., 1980)", Index)
 ("PONP800104", "Surrounding hydrophobicity in alpha-helix (Ponnuswamy et al., 1980)", Index)

julia> aaindex_by_id("JURD980101")

This returns an array of Index and AMatrix objects with the following respective interfaces:

struct Index <: AbstractAAIndex
    data::SVector{20}
    correlation::Dict{String, AbstractFloat}
    metadata::Metadata
end

struct AMatrix <: AbstractAAIndex
    rowids::String
    columnids::String
    data::Union{SHermitianCompact, SMatrix}
    metadata::Metadata
end

Entry metadata is stored in a separate struct with the following interface:

struct Metadata
    id::String
    description::String
    reference::Array{String}
    journal::String
    title::String
    authors::String
    comment::String
end

References

Kawashima, S., & Kanehisa, M. (2000). AAindex: amino acid index database. Nucleic acids research, 28(1), 374. https://doi.org/10.1093/nar/28.1.374

jowch/AAindex.jl

AAindex.jl

Usage

References