bio3d (version 2.3-3)

seqidentity: Percent Identity

Description

Determine the percent identity scores for aligned sequences.

Usage

seqidentity(alignment, normalize=TRUE, similarity=FALSE, ncore=1, nseg.scale=1)

Arguments

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.

similarity

logical, if TRUE sequence similarity is calculated instead of identity.

ncore

number of CPU cores used to do the calculation. ncore>1 requires package ‘parallel’ installed.

nseg.scale

split input data into specified number of segments prior to running multiple core calculation. See fit.xyz.

Value

Returns a numeric matrix with all pairwise identity values.

Details

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.

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

See Also

read.fasta, filter.identity, entropy, consensus

Examples

# NOT RUN {
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)
# }