SeqListSCOPe: Several sequences

In localScore: Package for Sequence Analysis by Local Score

Several sequences

Description

A vector of character strings

Usage

data(SeqListSCOPe)

Format

A list of 285 character strings with their entry codes as names

Source

Structural Classification Of Proteins database (SCOP). More precisely this data contain the 285 protein sequences of the data called "CF_scop2dom_20140205aa" with length from 31 to 404.

Examples

data(SeqListSCOPe)
head(SeqListSCOPe)
SeqListSCOPe[1]
nchar(SeqListSCOPe[1])
summary(sapply(SeqListSCOPe, nchar))
data(HydroScore)
MySeqScoreList <- lapply(SeqListSCOPe, FUN=CharSequence2ScoreSequence, HydroScore)
head(MySeqScoreList)
AA <- automatic_analysis(sequences=MySeqScoreList, model='iid')
AA[[1]]
# the p-value of the first 10 sequences 
sapply(AA, function(x){x$`p-value`})[1:10]
# the 20th smallest p-values
sort(sapply(AA, function(x){x$`p-value`}))[1:20]
which(sapply(AA, function(x){x$`p-value`})<0.05)
table(sapply(AA, function(x){x$`method`}))
# The maximum sequence length equals 404 so it here normal that the exact method is used for
# all the 606 sequences of the data base 
# Score distribution learned on the data set
scoreSequences2probabilityVector(MySeqScoreList)

localScore documentation built on April 3, 2025, 5:26 p.m.