logo RACCOON (Relative Amino aCid COmposition in dOmains and liNkers)   

Description

Amino acid composition has been used in several studies to deduce properties of all kinds of proteins, protein families and proteomes, but the difference in amino acid composition between domains has received little attention so far. Thus we studied the amino acid composition of domains with selected functions and their immediate linkers. We calculated the ratios of amino acid usage in each type of domain (or surrounding linker) versus all other domains (or linkers) in 38 proteomes from the three domains of life. These data can be visualized using a package which can be downloaded here (or in the Download section).

It allows any user to compare the mean amino acid composition of a specific domain to the mean amino acid composition of all domains, simultaneously for all available species. The analysis of amino acid composition is a valuable tool to assess another layer of information from protein sequences. The combined analysis of domains and linkers provides interesting insights into their compositional differences and can give further pieces of evidence for models of molecular interactions. Furthermore it could potentially help with annotation of domains and linkers in new proteomes or be used to discover duplicated regions as these may have a skewed amino acid composition.

Package content

    Files you need to use
  • README.txt → Readme file, with instructions about how to query the data.
  • app.R → The actual applet. To run with RStudio (read README file).

      • Extra files you do not need directly
  • "data" folder → Stores the raw data.
  • "www" folder → Figures for the "help" page.

    • How to

    STEP 1
    → Install Rstudio in your computer → https://www.rstudio.com/products/rstudio/download/
    → Install R in your computer → https://cran.r-project.org/

    STEP 2
    → Open Rstudio

    STEP 3
    → Type the following commands in Rstudio, to install the required packages
    install.packages("dplyr")
    install.packages("shiny")
    install.packages("tibble")
    install.packages("DT")
    install.packages("rmarkdown")
    install.packages("knitr")
    install.packages("ggvis")

    STEP 4
    → Open our source code in Rstudio
    File > Open File... > app.R

    STEP 5
    → Click on "Run App". The RACCOON application will start running shortly afterwards.

    Download

    Use it wisely: RACCOON package.

    Cite us

    Brune D, Andrade-Navarro MA, Mier P. Proteome-wide Comparison Between the Amino Acid Composition of Domains and Linkers. BMC Res Notes 2018 Feb 9;11(1):117. doi: 10.1186/s13104-018-3221-0. PMID:29426365.