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> results = search("hydrophobicity")
julia> specific_entry = search_id("ABCD123456")
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
key::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