# NOT RUN {
is.gap( c("G",".","X","-","G","K","S","T") )
# }
# NOT RUN {
aln <- read.fasta( system.file("examples/kif1a.fa",
package = "bio3d") )
##- Print only non-gap positions (i.e. no gaps in any sequence)
aln$ali[, !is.gap(aln) ]
##- Mask any existing gaps with an "X"
xaln <- aln
xaln$ali[ is.gap(xaln$ali) ]="X"
##- Read a new PDB and align its sequence to the existing masked alignment
pdb <- read.pdb( "1mkj" )
seq2aln(pdbseq(pdb), xaln, id = "1mkj")
# }
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