PredictHEC: Predict Protein Secondary Structure as Helix, Beta-Sheet, or...

In DECIPHER: Tools for curating, analyzing, and manipulating biological sequences

Description

Predicts 3-state protein secondary structure based on the primary (amino acid) sequence using the GOR IV method (Garnier et al., 1996).

Usage

PredictHEC(myAAStringSet,
           type = "states",
           windowSize = 7,
           background = c(H = -0.12, E = -0.25, C = 0.23),
           HEC_MI1 = NULL,
           HEC_MI2 = NULL)

Arguments

myAAStringSet	An AAStringSet object of sequences.
type	Character string indicating the type of results desired. This should be (an unambiguous abbreviation of) one of "states", "scores", or "probabilities".
windowSize	Numeric specifying the number of residues to the left or right of the center position to use in the prediction.
background	Numeric vector with the background “scores” for each of the three states (H, E, and C).
HEC_MI1	An array of dimensions 20 x 21 x 3 giving the mutual information for single residues.
HEC_MI2	An array of dimensions 20 x 20 x 21 x 21 x 3 giving the mutual information for pairs of residues.

Details

The GOR (Garnier-Osguthorpe-Robson) method is an information-theory method for prediction of secondary structure based on the primary sequence of a protein. Version IV of the method makes 3-state predictions based on the mutual information contained in single residues and pairs of residues within windowSize residues of the position being assigned. This approach is about 65% accurate, and is one of the most accurate methods for assigning secondary structure that only use a single sequence. This implementation of GOR IV does not use decision constants or the number of contiguous states when assigning the final state. Note that characters other than the standard 20 amino acids are not assigned a state.

Value

If type is "states" (the default), then the output is a character vector with the secondary structure assignment ("H", "E", or "C") for each residue in myAAStringSet.

Otherwise, the output is a list with one element for each sequence in myAAStringSet. Each list element contains a matrix of dimension 3 (H, E, or C) by the number of residues in the sequence. If type is "scores", then values in the matrix represent log-odds “scores”. If type is "probabilities" then the values represent the normalized probabilities of the three states at a position.

Author(s)

Erik Wright [e-mail]

References

Garnier, J., Gibrat, J. F., & Robson, B. (1996). GOR method for predicting protein secondary structure from amino acid sequence. Methods in Enzymology, 266, 540-553.

See Also

HEC_MI1, HEC_MI2, PredictDBN

Examples

fas <- system.file("extdata", "50S_ribosomal_protein_L2.fas", package="DECIPHER")
dna <- readDNAStringSet(fas)
aa <- translate(dna)
hec <- PredictHEC(aa)
head(hec)

Example output

Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: RSQLite
[1] "CCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCEEEECCCCCCCCCCCCEEEEEECCCCCCEEEEEHHHCCCCCCHHHHHHHECCCCCCHHHEEEEECCCCCCEEEECCCCCCCCCEEEHHHHHHHHHCCCCCCCCCCCCCEECHHEEECCCCCEEEEECCCCEEEECCCCCHEEEHHCCCCCEEEECCCCEEECCCCCCCCHHHEHCCCCCCEEECCCCCCEEEEECCCCCCCCCCCCEECCCCCCECCCCECCCCCEEECCCCCCHEEHHCCC" 
[2] "CCCCECCCCCCCCCEEEEEEECEEECCCCCCHEEEEECCCCCCCCCCCEEEEEECCCCCCEEEEEEECCCCCCCCCEEEEEEECCCCCHHHEEHHHHCCCCEEEECCCCCCEEEEEECCCCCCHHHCCCCCCCCCCCCEEEEEEECCCCCCHEEEEHCCCHHEECCCCCCEEEEECCCCCCEEEEEECEEEEEECCCCCHHHHHHCCCCCEEEECCCCCCCEEEECCCCCCCCCCCCEECCCCCCCCHHHHHHCCCCCCCCCCCCHHHHHHHCC"
[3] "CCCCECCCCCCCCCEEEEEEECEEECCCCCCHEEEEECCCCCCCCCCCEEEEEECCCCCCEEEEEEECCCCCCCCCEEEEEEECCCCCHHHEEHHHHCCCCEEEECCCCCCEEEEEECCCCCCHHHCCCCCCCCCCCCEEEEEEECCCCCCHEEEEHCCCHHEECCCCCCEEEEECCCCCCEEEEEECEEEEEECCCCCHHHHHHCCCCCEEEECCCCCCCEEEECCCCCCCCCCCCEECCCCCCCCHHHHHHCCCCCCCCCCCCHHHHHHHCC"
[4] "CCCCECCCCCCCCCEEEEEEECEEECCCCCCHEEEEECCCCCCCCCCCEEEEEECCCCCCEEEEEEECCCCCCCCCEEEEEEECCCCCHHHEEHHHHCCCCEEEECCCCCCEEEEEECCCCCCHHHCCCCCCCCCCCCEEEEEEECCCCCCHEEEEHCCCHHEECCCCCCEEEEECCCCCCEEEEEECEEEEEECCCCCHHHHHHCCCCCEEEECCCCCCCEEEECCCCCCCCCCCCEECCCCCCCCHHHHHHCCCCCCCCCCCCHHHHHHHCC"
[5] "CCEEEECCCCCCCEEEEEEECCCCCCCCCCCCEECCCCCCCCCCCCCEEEEEEECCCCCCEEEEHHHHCCCCCCHHHHHHHCCCCCCHHHHEEEEHCCCCHEEEECCCCCCCCCEEECCCCCCEECCCCCCCCCCCCCCEEEEEEECCCCCCEEEHHCCHHEEEEECCCCCEEEEHCCCHHHHHHHHHCEEECCCCCCHHHHHHHHHCCCCCECCCCCCEEECECCCCCCCCCCCCCCECCCCCCCCEEEECCCCCEECCCCCCEEEEECCCC" 
[6] "CCEEEECCCCCCCEEEEEEECCCCCCCCCCCCEECCCCCCCCCCCCCEEEEEEECCCCCCEEEEHHHHCCCCCCHHHHHHHCCCCCCHHHHEEEEHCCCCHEEEECCCCCCCCCEEECCCCCCEECCCCCCCCCCCCCCEEEEEEECCCCCCEEEHHCCHHEEEEECCCCCEEEEHCCCHHHHHHHHHCEEECCCCCCHHHHHHHHHCCCCCECCCCCCEEECECCCCCCCCCCCCCCECCCCCCCCEEEECCCCCEECCCCCCEEEEECCCC" 

DECIPHER documentation built on Nov. 8, 2020, 8:30 p.m.