localScore (version 1.0.6)

ShortSeq: Short protein sequence

Description

A short protein sequence of 31 amino acids corresponding to Q09FU3.fasta query in UniProt Data base.

Usage

ShortSeq

Format

A character string with 31 characters "MLTITSYFGFLLAALTITSVLFIGLNKIRLI"

Examples

# NOT RUN {
data(ShortSeq)
ShortSeq
nchar(ShortSeq)
data(dico) 
SeqScore=CharSequence2ScoreSequence(ShortSeq,dico)
SeqScore
localScoreC(SeqScore)$localScore
LS=localScoreC(SeqScore)$localScore[1]
prob1 = scoreSequences2probabilityVector(list(SeqScore))
daudin(localScore = LS, sequence_length = nchar(ShortSeq),
               score_probabilities = prob1,
               sequence_min = min(SeqScore),
               sequence_max = max(SeqScore))
score=-5:5
prob2=c(0.15,0.15,0.1,0.1,0.0,0.05,0.15,0.05,0.2,0.0,0.05)
sum(prob2*score)
karlin(localScore = LS, sequence_length = nchar(ShortSeq),
score_probabilities = prob2,
sequence_min = min(SeqScore),
sequence_max = max(SeqScore))
# }