seqidentity. bio3d 2.3-0

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.

Description

Determine the percent identity scores for aligned sequences.

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.

References

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

Examples


attach(kinesin)

The following objects are masked from transducin:

    annotation, core, pdbs


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,]) )

      [,1]  [,2]
[1,] 1.000 0.461
[2,] 0.461 1.000


detach(kinesin)

Author

Barry Grant

Percent Identity