Produces a schematic representation of a multiple sequence alignment.

# S3 method for fasta
plot(x, hc = TRUE, labels = xid, cex.lab = 0.7, xlab = "Alignment index", main = "Sequence Alignment Overview", mar4 = 4, ...) ## Arguments x multiple sequence alignement of class ‘fasta’ as obtained from seqaln. logical, if TRUE plot a dendrogram on the left side. Alternatively, an object obtained from hclust can be provided. labels corresponding to each row in the alignment. scaling factor for the labels. label for x-axis. a main title for the plot. margin size for the labels. additional arguments passed to function hclust. ## Details plot.fasta is a utility function for producting a schematic representation of a multiple sequence alignment. ## Value Called for its effect. ## References Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696. ## Author Lars Skjaerven ## See also seqaln, read.fasta, entropy, aln2html. ## Examples # Read alignment aln <- read.fasta(system.file("examples/kif1a.fa",package="bio3d")) ## alignment plot plot(aln, labels=basename.pdb(alnid))

## Works also for a 'pdbs' object
attach(transducin)
plot(pdbs)

detach(transducin)

if (FALSE) {
infile <- "http://pfam.xfam.org/family/PF00071/alignment/seed/format?format=fasta"