seqidentity.Rd
Determine the percent identity scores for aligned sequences.
seqidentity(alignment, normalize=TRUE, similarity=FALSE, ncore=1, nseg.scale=1)
alignment  sequence alignment obtained from


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.

nseg.scale  split input data into specified number of segments
prior to running multiple core calculation. See 
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.
Returns a numeric matrix with all pairwise identity values.
Grant, B.J. et al. (2006) Bioinformatics 22, 26952696.
Barry Grant
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")#> [,1] [,2] #> [1,] 1.000 0.461 #> [2,] 0.461 1.000detach(kinesin)