Percent Identity
Determine the percent identity scores for aligned sequences.
seqidentity(alignment, normalize=TRUE, similarity=FALSE, ncore=1, nseg.scale=1)
alignment |
sequence alignment obtained from
|
normalize |
logical, if TRUE output is normalized to values between 0 and 1 otherwise percent identity is returned. |
similarity |
logical, if TRUE sequence similarity is calculated instead of identity. |
ncore |
number of CPU cores used to do the calculation.
|
nseg.scale |
split input data into specified number of segments
prior to running multiple core calculation. See |
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.
attach(kinesin)
ide.mat <- seqidentity(pdbs)
# 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
seqidentity( rbind(pdbs$ali[1,], pdbs$ali[15,]) )
detach(kinesin)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.