BioSeqClass (version 1.30.0)

featureSSC: 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.....

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)  
}