| identity {bio3d} | R Documentation |
Determine the percent identity scores for aligned sequences.
identity(alignment, normalize=TRUE)
alignment |
sequence alignment obtained from
read.fasta or an alignment character matrix. |
normalize |
logical, if TRUE output is normalized to values between 0 and 1 otherwise percent identity is returned. |
The percent identity value is a single numeric score determined for each pair of aligned sequences. It measures the number of identical residues (“matches”) in relation to the length of the alignment.
Returns a numeric matrix with all pairwise identity values.
Barry Grant
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
read.fasta, ide.filter, entropy, consensus
## Not run:
#aln <- read.fasta( system.file("examples/kinesin_xray.fa",
# package = "bio3d") )
## End(Not run)
data(kinesin)
attach(kinesin)
ide.mat <- identity(aln)
# Plot identity matrix
plot.dmat(ide.mat, color.palette=mono.colors,
main="Sequence Identity", xlab="Structure No.",
ylab="Structure No.")
# Histogram of pairwise identity values
hist(ide.mat[upper.tri(ide.mat)], breaks=30,xlim=c(0,1),
main="Sequence Identity", xlab="Identity")
# Compare two sequences
identity( rbind(aln$ali[1,], aln$ali[20,]) )