featureSSC {BioSeqClass} | R Documentation

## Feature Coding by secondary structure

### Description

It is suitable for peptides with odd residues and the central residue has important role.

### Usage

      featureSSC(secondaryStructure, confidenceScore)

      # secondary structure from DSSP database
      getDSSP(pdb)
      # Protein secondary structure prediction
      predictPROTEUS(seq,proteus2.organism="euk")

### Arguments

`secondaryStructure` | a string vector for the protein secondary structure. It is consisted of three kinds of secondary structures: H = Helix, E = Beta Strand, C = Coil.
`confidenceScore` | a string vector for the confidence score of secondary structure prediction (0-9, 0 = low, 9 = high).
`pdb` | a string vector for the name of pdb structure. (e.g. "43ca")
`seq` | a string vector for the protein, DNA, or RNA sequences.
`proteus2.organism` | a string for the organism of proteus2 program. This must be one of the strings "gram-", "gram+", "euk".

### Details

`featureSSC` codes for the secondary structure of the central residue of peptides. It is suitable for peptides with odd residues and the central residue has important role.

`getDSSP` returns a vector of secondary structure extracted from DSSP database (http://swift.cmbi.ru.nl/gv/dssp/).

`predictPROTEUS` predicts secondary structure based on protein sequence using following methods : "PROTEUS2", "PSIPRED", "JNET", "TRANSSEC", "JURY-OF-EXPERTS PREDICTION". Parameter "proteus2.organism" can be "gram-" for "Gram negative prokaryote", "gram+" for "Gram positive prokaryote", "euk" for "Eukaryote". It returns.....

### Author(s)

Hong Li

### Examples

    if(interactive()){
      file = file.path(path.package("BioSeqClass"), "example", "acetylation_K.fasta")
      tmp = readAAStringSet(file)
      proteinSeq = as.character(tmp)

      DSSP1 = getDSSP(c("108l","43ca"))
      DSSP2 = getDSSP(c("108l","43ca","aaaa"))

      ## Predict protein secordary strucutre
      PROTEUS = predictPROTEUS(proteinSeq[1:2],proteus2.organism="euk")

      ## Use general feature conding functions to codes protein secordary strucutre
      secondaryStructure = sapply(PROTEUS,function(x){paste(x[["PROTEUS2"]]$SecondaryStructure,collapse="")})
      confidenceScore = sapply(PROTEUS,function(x){paste(x[["PROTEUS2"]]$ConfidenceScore,collapse="")})
      SSCTD = featureCTD(secondaryStructure, class=list("H"="H","E"="E","C"="C"))
      # Codes for peptides which have equal length and their central residues are important
      secondaryStructure = sapply(PROTEUS,function(x){sub.seq(paste(x[["PROTEUS2"]]$SecondaryStructure,collapse=""), 1, 11)})
      confidenceScore = sapply(PROTEUS,function(x){sub.seq(paste(x[["PROTEUS2"]]$ConfidenceScore,collapse=""), 1, 11)})

      SS1 = featureSSC(secondaryStructure, confidenceScore)
    }

[Package BioSeqClass version 1.40.0 Index]