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#' Disorder-based Substitution Matrices.
#'
#' \strong{The Disorder40, Disorder60, and Disorder85 Matrices were
#' developed and described in
#' \href{https://doi.org/10.1093/molbev/msp277}{Brown et al. (2009)}.} \cr
#' In short: There are substitution scoring matrices used to align proteins
#' or regions which experience intrinsic disorder. The matrices were
#' calculated using pairwise sequence alignments of protein families
#' which here identified from 287 experimentally confirmed Intrinsically
#' Disordered Proteins (IDPs). The IDPs contained at least 30 sequential
#' residues of intrinsic disorder and protein families were found using
#' BLAST.\cr There was not a comprehensive comparison to other frequently
#' used substitution matrices (like BLOSUM and PAM) in terms of improving IDP
#' sequence alignments. The authors note that the purpose of these
#' matrices were made to compare evolutionary characteristics of disordered
#' and ordered proteins. Please see the source material for additional
#' information.\cr \cr
#' \href{https://doi.org/10.1038/s41598-019-52532-8}{Trivedi and
#' Nagarajaram (2019)} compared EDSSMat62 against all three Disordered
#' Matrices. Disorder40 and Disorder85 attain lower E-values for
#' highly disordered proteins, on average, when compared to EDSSMat62.
#' EDSSMat62 attained lower E-values when compared to Disorder60 for aligning
#' highly disordered proteins.
#' EDSSMat62 preforms better than all three Disorder matrices for IDPs
#' enriched in ordered regions. Please
#' see the referenced paper, specifically Supplementary Figures S18-20, for
#' additional information and original comparison. \cr \cr
#' Additionally, please cite the source article when using Disorder40,
#' Disorder60, or Disorder85.
#'
#' @format All matrices are symmetric. 24 residues are represented:
#' \itemize{
#' \item Each of the standard 20 standard amino acids
#' \item Four ambiguous residues:
#' \itemize{
#' \item B: Asparagine or Aspartic Acid (Asx)
#' \item Z: Glutamine or Glutamic Acid (Glx)
#' \item X: Unspecified or unknown amino acid
#' \item *: Stop
#' }
#' }
#'
#' @section Optimal Gap Parameters:
#' As mentioned in the Description, the intended use of these matrices was
#' not to improve sequence alignments. Therefore, no gap penalty values are
#' provided.
#'
#' It should also be noted that a more recent work,
#' \href{https://doi.org/10.1038/s41598-019-52532-8}{Trivedi and
#' Nagarajaram (2019)}, determined optimal parameters based on the disordered
#' content of query sequences, as reported in the paper's Supplementary Table
#' S5.
#' \tabular{ccccccc}{
#' Matrix Name \tab Gap Open (LD) \tab Gap Extension (LD) \tab Gap Open (MD)
#' \tab Gap Extension (MD) \tab Gap Open (HD) \tab Gap Extension (HD) \cr
#' Disorder40 \tab -20 \tab -1 \tab -7 \tab -1 \tab -7 \tab -1 \cr
#' Disorder60 \tab -20 \tab -1 \tab -16 \tab -1 \tab -11 \tab -2 \cr
#' Disorder85 \tab -20 \tab -1 \tab -16 \tab -1 \tab -7 \tab -2}
#' Please see the referenced paper for additional information and original
#' reporting. Additionally, please see \code{\link{EDSSMat}}.
#' @source Brown, C. J., Johnson, A. K., & Daughdrill, G. W. (2009).
#' Comparing Models of Evolution for Ordered and Disordered Proteins.
#' Molecular Biology and Evolution, 27(3), 609-621.
#' \href{https://doi.org/10.1093/molbev/msp277}{doi:10.1093/molbev/msp277}
#' @section Additional Reference:
#' Trivedi, R., Nagarajaram, H.A. Amino acid substitution scoring
#' matrices specific to intrinsically disordered regions in proteins. Sci
#' Rep 9, 16380 (2019).
#' \url{https://doi.org/10.1038/s41598-019-52532-8}
#' @family IDP-based Substitution Matrices
#' @seealso Disordered Matrices Vignette within the idpr package and EDSSMat62
#' @name DisorderMat
NULL
#' @rdname DisorderMat
"Disorder40"
#' @rdname DisorderMat
"Disorder60"
#' @rdname DisorderMat
"Disorder85"
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