featureSSC {BioSeqClass} | R Documentation |
It is suitable for peptides with odd residues and the central residue has important role.
featureSSC(secondaryStructure, confidenceScore) # secondary structure from DSSP database getDSSP(pdb) # Protein secondary structure prediction predictPROTEUS(seq,proteus2.organism="euk")
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". |
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.....
Hong Li
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) }