Percent Identity

Description

Determine the percent identity scores for aligned sequences.

Usage

  identity(alignment)

Arguments

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, ide.filter, entropy, consensus

Examples

## 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,]) )