Percent Identity

Determine the percent identity scores for aligned sequences.

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.

References

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

Author

Barry Grant

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,]) )
#>       [,1]  [,2]
#> [1,] 1.000 0.461
#> [2,] 0.461 1.000

detach(kinesin)