seqidentity {bio3d}

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.

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.

Value

Returns a numeric matrix with all pairwise identity values.

Author(s)

Barry Grant

References

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

See Also

read.fasta, filter.identity, entropy, consensus

Examples

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)