is.gap(x, gap.char = c("-", "."))
seqaln,
pdbaln etc. Test for the presence of gap characters.
Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.
During alignment, gaps are introduced into sequences that are believed to have undergone deletions or insertions with respect to other sequences in the alignment. These gaps, often referred to as indels, can be represented with ‘NA’, ‘-’ or ‘.’ characters.
This function provides a simple test for the presence of such characters, or indeed any set of user defined characters set by the ‘gap.char’ argument.
is.gap( c("G",".","X","-","G","K","S","T") )[1] FALSE TRUE FALSE TRUE FALSE FALSE FALSE FALSEaln <- 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) ][,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] http://www.rcsb.org/pdb/files/1bg2.pdb "N" "I" "K" "V" "M" "C" "R" "F" http://www.rcsb.org/pdb/files/1i6i.pdb "S" "V" "K" "V" "A" "V" "R" "V" http://www.rcsb.org/pdb/files/1i5s.pdb "S" "V" "K" "V" "A" "V" "R" "V" http://www.rcsb.org/pdb/files/2ncd.pdb "N" "I" "R" "V" "F" "C" "R" "I" [,9] [,10] [,11] [,12] [,13] [,14] [,15] http://www.rcsb.org/pdb/files/1bg2.pdb "R" "P" "L" "N" "E" "S" "E" http://www.rcsb.org/pdb/files/1i6i.pdb "R" "P" "F" "N" "S" "R" "E" http://www.rcsb.org/pdb/files/1i5s.pdb "R" "P" "F" "N" "S" "R" "E" http://www.rcsb.org/pdb/files/2ncd.pdb "R" "P" "P" "L" "E" "S" "E" [,16] [,17] [,18] [,19] [,20] [,21] http://www.rcsb.org/pdb/files/1bg2.pdb "V" "N" "R" "G" "D" "Y" http://www.rcsb.org/pdb/files/1i6i.pdb "M" "S" "R" "D" "S" "C" http://www.rcsb.org/pdb/files/1i5s.pdb "M" "S" "R" "D" "S" "C" http://www.rcsb.org/pdb/files/2ncd.pdb "E" "N" "R" "M" "C" "C" [,22] [,23] [,24] [,25] [,26] [,27] http://www.rcsb.org/pdb/files/1bg2.pdb "I" "A" "K" "F" "Q" "G" http://www.rcsb.org/pdb/files/1i6i.pdb "I" "I" "Q" "M" "S" "G" http://www.rcsb.org/pdb/files/1i5s.pdb "I" "I" "Q" "M" "S" "G" http://www.rcsb.org/pdb/files/2ncd.pdb "T" "W" "T" "Y" "H" "D" [,28] [,29] [,30] [,31] [,32] [,33] http://www.rcsb.org/pdb/files/1bg2.pdb "E" "D" "T" "V" "V" "I" http://www.rcsb.org/pdb/files/1i6i.pdb "S" "T" "T" "T" "I" "V" http://www.rcsb.org/pdb/files/1i5s.pdb "S" "T" "T" "T" "I" "V" http://www.rcsb.org/pdb/files/2ncd.pdb "E" "S" "T" "V" "I" "D" [,34] [,35] [,36] [,37] [,38] [,39] http://www.rcsb.org/pdb/files/1bg2.pdb "A" "S" "K" "P" "Y" "A" http://www.rcsb.org/pdb/files/1i6i.pdb "N" "P" "K" "S" "F" "S" http://www.rcsb.org/pdb/files/1i5s.pdb "N" "P" "K" "S" "F" "S" http://www.rcsb.org/pdb/files/2ncd.pdb "A" "Q" "A" "I" "F" "S" [,40] [,41] [,42] [,43] [,44] [,45] http://www.rcsb.org/pdb/files/1bg2.pdb "F" "D" "R" "V" "F" "Q" http://www.rcsb.org/pdb/files/1i6i.pdb "F" "D" "Y" "S" "Y" "W" http://www.rcsb.org/pdb/files/1i5s.pdb "F" "D" "Y" "S" "Y" "W" http://www.rcsb.org/pdb/files/2ncd.pdb "F" "D" "Q" "V" "F" "H" [,46] [,47] [,48] [,49] [,50] [,51] http://www.rcsb.org/pdb/files/1bg2.pdb "S" "S" "T" "S" "Q" "E" http://www.rcsb.org/pdb/files/1i6i.pdb "S" "H" "A" "S" "Q" "K" http://www.rcsb.org/pdb/files/1i5s.pdb "S" "H" "A" "S" "Q" "K" http://www.rcsb.org/pdb/files/2ncd.pdb "P" "L" "S" "S" "Q" "S" [,52] [,53] [,54] [,55] [,56] [,57] http://www.rcsb.org/pdb/files/1bg2.pdb "Q" "V" "Y" "D" "C" "A" http://www.rcsb.org/pdb/files/1i6i.pdb "Q" "V" "Y" "D" "I" "G" http://www.rcsb.org/pdb/files/1i5s.pdb "Q" "V" "Y" "D" "I" "G" http://www.rcsb.org/pdb/files/2ncd.pdb "D" "I" "F" "E" "M" "V" [,58] [,59] [,60] [,61] [,62] [,63] http://www.rcsb.org/pdb/files/1bg2.pdb "K" "K" "I" "V" "K" "D" http://www.rcsb.org/pdb/files/1i6i.pdb "E" "E" "M" "L" "Q" "H" http://www.rcsb.org/pdb/files/1i5s.pdb "E" "E" "M" "L" "Q" "H" http://www.rcsb.org/pdb/files/2ncd.pdb "S" "P" "L" "I" "Q" "S" [,64] [,65] [,66] [,67] [,68] [,69] http://www.rcsb.org/pdb/files/1bg2.pdb "V" "L" "E" "G" "Y" "N" http://www.rcsb.org/pdb/files/1i6i.pdb "A" "F" "E" "G" "Y" "N" http://www.rcsb.org/pdb/files/1i5s.pdb "A" "F" "E" "G" "Y" "N" http://www.rcsb.org/pdb/files/2ncd.pdb "A" "L" "D" "G" "Y" "N" [,70] [,71] [,72] [,73] [,74] [,75] http://www.rcsb.org/pdb/files/1bg2.pdb "G" "T" "I" "F" "A" "Y" http://www.rcsb.org/pdb/files/1i6i.pdb "V" "C" "I" "F" "A" "Y" http://www.rcsb.org/pdb/files/1i5s.pdb "V" "C" "I" "F" "A" "Y" http://www.rcsb.org/pdb/files/2ncd.pdb "I" "C" "I" "F" "A" "Y" [,76] [,77] [,78] [,79] [,80] [,81] http://www.rcsb.org/pdb/files/1bg2.pdb "G" "Q" "T" "S" "S" "G" http://www.rcsb.org/pdb/files/1i6i.pdb "G" "Q" "T" "G" "A" "G" http://www.rcsb.org/pdb/files/1i5s.pdb "G" "Q" "T" "G" "A" "G" http://www.rcsb.org/pdb/files/2ncd.pdb "G" "Q" "T" "G" "S" "G" [,82] [,83] [,84] [,85] [,86] [,87] http://www.rcsb.org/pdb/files/1bg2.pdb "K" "T" "H" "T" "M" "E" http://www.rcsb.org/pdb/files/1i6i.pdb "K" "S" "Y" "T" "M" "M" http://www.rcsb.org/pdb/files/1i5s.pdb "K" "S" "Y" "T" "M" "M" http://www.rcsb.org/pdb/files/2ncd.pdb "K" "T" "Y" "T" "M" "D" [,88] [,89] [,90] [,91] [,92] [,93] http://www.rcsb.org/pdb/files/1bg2.pdb "G" "K" "E" "G" "M" "G" http://www.rcsb.org/pdb/files/1i6i.pdb "G" "K" "D" "Q" "Q" "G" http://www.rcsb.org/pdb/files/1i5s.pdb "G" "K" "D" "Q" "Q" "G" http://www.rcsb.org/pdb/files/2ncd.pdb "G" "V" "E" "S" "V" "G" [,94] [,95] [,96] [,97] [,98] [,99] http://www.rcsb.org/pdb/files/1bg2.pdb "I" "I" "P" "R" "I" "V" http://www.rcsb.org/pdb/files/1i6i.pdb "I" "I" "P" "Q" "L" "C" http://www.rcsb.org/pdb/files/1i5s.pdb "I" "I" "P" "Q" "L" "C" http://www.rcsb.org/pdb/files/2ncd.pdb "V" "I" "P" "R" "T" "V" [,100] [,101] [,102] [,103] [,104] http://www.rcsb.org/pdb/files/1bg2.pdb "Q" "D" "I" "F" "N" http://www.rcsb.org/pdb/files/1i6i.pdb "E" "D" "L" "F" "S" http://www.rcsb.org/pdb/files/1i5s.pdb "E" "D" "L" "F" "S" http://www.rcsb.org/pdb/files/2ncd.pdb "D" "L" "L" "F" "D" [,105] [,106] [,107] [,108] [,109] http://www.rcsb.org/pdb/files/1bg2.pdb "Y" "I" "Y" "S" "M" http://www.rcsb.org/pdb/files/1i6i.pdb "R" "I" "N" "D" "T" http://www.rcsb.org/pdb/files/1i5s.pdb "R" "I" "N" "D" "T" http://www.rcsb.org/pdb/files/2ncd.pdb "S" "I" "R" "G" "Y" [,110] [,111] [,112] [,113] [,114] http://www.rcsb.org/pdb/files/1bg2.pdb "D" "E" "N" "L" "E" http://www.rcsb.org/pdb/files/1i6i.pdb "T" "N" "D" "N" "S" http://www.rcsb.org/pdb/files/1i5s.pdb "T" "N" "D" "N" "S" http://www.rcsb.org/pdb/files/2ncd.pdb "R" "N" "L" "G" "E" [,115] [,116] [,117] [,118] [,119] http://www.rcsb.org/pdb/files/1bg2.pdb "F" "H" "I" "K" "V" http://www.rcsb.org/pdb/files/1i6i.pdb "Y" "S" "V" "E" "V" http://www.rcsb.org/pdb/files/1i5s.pdb "Y" "S" "V" "E" "V" http://www.rcsb.org/pdb/files/2ncd.pdb "Y" "E" "I" "K" "A" [,120] [,121] [,122] [,123] [,124] http://www.rcsb.org/pdb/files/1bg2.pdb "S" "Y" "F" "E" "I" http://www.rcsb.org/pdb/files/1i6i.pdb "S" "Y" "M" "E" "I" http://www.rcsb.org/pdb/files/1i5s.pdb "S" "Y" "M" "E" "I" http://www.rcsb.org/pdb/files/2ncd.pdb "T" "F" "L" "E" "I" [,125] [,126] [,127] [,128] [,129] http://www.rcsb.org/pdb/files/1bg2.pdb "Y" "L" "D" "K" "I" http://www.rcsb.org/pdb/files/1i6i.pdb "Y" "C" "E" "R" "V" http://www.rcsb.org/pdb/files/1i5s.pdb "Y" "C" "E" "R" "V" http://www.rcsb.org/pdb/files/2ncd.pdb "Y" "N" "E" "V" "L" [,130] [,131] [,132] [,133] [,134] http://www.rcsb.org/pdb/files/1bg2.pdb "R" "D" "L" "L" "D" http://www.rcsb.org/pdb/files/1i6i.pdb "R" "D" "L" "L" "N" http://www.rcsb.org/pdb/files/1i5s.pdb "R" "D" "L" "L" "N" http://www.rcsb.org/pdb/files/2ncd.pdb "Y" "D" "L" "L" "N" [,135] [,136] [,137] [,138] [,139] http://www.rcsb.org/pdb/files/1bg2.pdb "V" "S" "K" "T" "N" http://www.rcsb.org/pdb/files/1i6i.pdb "P" "K" "N" "K" "N" http://www.rcsb.org/pdb/files/1i5s.pdb "P" "K" "N" "K" "N" http://www.rcsb.org/pdb/files/2ncd.pdb "E" "Q" "K" "D" "E" [,140] [,141] [,142] [,143] [,144] http://www.rcsb.org/pdb/files/1bg2.pdb "L" "S" "V" "H" "E" http://www.rcsb.org/pdb/files/1i6i.pdb "L" "R" "V" "R" "E" http://www.rcsb.org/pdb/files/1i5s.pdb "L" "R" "V" "R" "E" http://www.rcsb.org/pdb/files/2ncd.pdb "I" "R" "M" "A" "K" [,145] [,146] [,147] [,148] [,149] http://www.rcsb.org/pdb/files/1bg2.pdb "D" "K" "N" "R" "V" http://www.rcsb.org/pdb/files/1i6i.pdb "H" "P" "L" "L" "G" http://www.rcsb.org/pdb/files/1i5s.pdb "H" "P" "L" "L" "G" http://www.rcsb.org/pdb/files/2ncd.pdb "N" "N" "K" "N" "D" [,150] [,151] [,152] [,153] [,154] http://www.rcsb.org/pdb/files/1bg2.pdb "P" "Y" "V" "K" "G" http://www.rcsb.org/pdb/files/1i6i.pdb "P" "Y" "V" "E" "D" http://www.rcsb.org/pdb/files/1i5s.pdb "P" "Y" "V" "E" "D" http://www.rcsb.org/pdb/files/2ncd.pdb "I" "Y" "V" "S" "N" [,155] [,156] [,157] [,158] [,159] http://www.rcsb.org/pdb/files/1bg2.pdb "C" "T" "E" "R" "F" http://www.rcsb.org/pdb/files/1i6i.pdb "L" "S" "K" "L" "A" http://www.rcsb.org/pdb/files/1i5s.pdb "L" "S" "K" "L" "A" http://www.rcsb.org/pdb/files/2ncd.pdb "I" "T" "E" "E" "T" [,160] [,161] [,162] [,163] [,164] http://www.rcsb.org/pdb/files/1bg2.pdb "V" "C" "S" "P" "D" http://www.rcsb.org/pdb/files/1i6i.pdb "V" "T" "S" "Y" "N" http://www.rcsb.org/pdb/files/1i5s.pdb "V" "T" "S" "Y" "N" http://www.rcsb.org/pdb/files/2ncd.pdb "V" "L" "D" "P" "N" [,165] [,166] [,167] [,168] [,169] http://www.rcsb.org/pdb/files/1bg2.pdb "E" "V" "M" "D" "T" http://www.rcsb.org/pdb/files/1i6i.pdb "D" "I" "Q" "D" "L" http://www.rcsb.org/pdb/files/1i5s.pdb "D" "I" "Q" "D" "L" http://www.rcsb.org/pdb/files/2ncd.pdb "H" "L" "R" "H" "L" [,170] [,171] [,172] [,173] [,174] http://www.rcsb.org/pdb/files/1bg2.pdb "I" "D" "E" "G" "K" http://www.rcsb.org/pdb/files/1i6i.pdb "M" "D" "S" "G" "N" http://www.rcsb.org/pdb/files/1i5s.pdb "M" "D" "S" "G" "N" http://www.rcsb.org/pdb/files/2ncd.pdb "M" "H" "T" "A" "K" [,175] [,176] [,177] [,178] [,179] http://www.rcsb.org/pdb/files/1bg2.pdb "S" "N" "R" "H" "V" http://www.rcsb.org/pdb/files/1i6i.pdb "K" "A" "R" "T" "V" http://www.rcsb.org/pdb/files/1i5s.pdb "K" "A" "R" "T" "V" http://www.rcsb.org/pdb/files/2ncd.pdb "M" "N" "R" "A" "T" [,180] [,181] [,182] [,183] [,184] http://www.rcsb.org/pdb/files/1bg2.pdb "A" "V" "T" "N" "M" http://www.rcsb.org/pdb/files/1i6i.pdb "A" "A" "T" "N" "M" http://www.rcsb.org/pdb/files/1i5s.pdb "A" "A" "T" "N" "M" http://www.rcsb.org/pdb/files/2ncd.pdb "A" "S" "T" "A" "G" [,185] [,186] [,187] [,188] [,189] http://www.rcsb.org/pdb/files/1bg2.pdb "N" "E" "H" "S" "S" http://www.rcsb.org/pdb/files/1i6i.pdb "N" "E" "T" "S" "S" http://www.rcsb.org/pdb/files/1i5s.pdb "N" "E" "T" "S" "S" http://www.rcsb.org/pdb/files/2ncd.pdb "N" "E" "R" "S" "S" [,190] [,191] [,192] [,193] [,194] http://www.rcsb.org/pdb/files/1bg2.pdb "R" "S" "H" "S" "I" http://www.rcsb.org/pdb/files/1i6i.pdb "R" "S" "H" "A" "V" http://www.rcsb.org/pdb/files/1i5s.pdb "R" "S" "H" "A" "V" http://www.rcsb.org/pdb/files/2ncd.pdb "R" "S" "H" "A" "V" [,195] [,196] [,197] [,198] [,199] http://www.rcsb.org/pdb/files/1bg2.pdb "F" "L" "I" "N" "V" http://www.rcsb.org/pdb/files/1i6i.pdb "F" "N" "I" "I" "F" http://www.rcsb.org/pdb/files/1i5s.pdb "F" "N" "I" "I" "F" http://www.rcsb.org/pdb/files/2ncd.pdb "T" "K" "L" "E" "L" [,200] [,201] [,202] [,203] [,204] http://www.rcsb.org/pdb/files/1bg2.pdb "K" "Q" "E" "N" "T" http://www.rcsb.org/pdb/files/1i6i.pdb "T" "Q" "K" "R" "H" http://www.rcsb.org/pdb/files/1i5s.pdb "T" "Q" "K" "R" "H" http://www.rcsb.org/pdb/files/2ncd.pdb "I" "G" "R" "H" "A" [,205] [,206] [,207] [,208] [,209] http://www.rcsb.org/pdb/files/1bg2.pdb "Q" "T" "E" "Q" "K" http://www.rcsb.org/pdb/files/1i6i.pdb "D" "A" "T" "T" "E" http://www.rcsb.org/pdb/files/1i5s.pdb "D" "A" "T" "T" "E" http://www.rcsb.org/pdb/files/2ncd.pdb "E" "K" "Q" "E" "I" [,210] [,211] [,212] [,213] [,214] http://www.rcsb.org/pdb/files/1bg2.pdb "L" "S" "G" "K" "L" http://www.rcsb.org/pdb/files/1i6i.pdb "K" "V" "S" "K" "I" http://www.rcsb.org/pdb/files/1i5s.pdb "K" "V" "S" "K" "I" http://www.rcsb.org/pdb/files/2ncd.pdb "S" "V" "G" "S" "I" [,215] [,216] [,217] [,218] [,219] http://www.rcsb.org/pdb/files/1bg2.pdb "Y" "L" "V" "D" "L" http://www.rcsb.org/pdb/files/1i6i.pdb "S" "L" "V" "D" "L" http://www.rcsb.org/pdb/files/1i5s.pdb "S" "L" "V" "D" "L" http://www.rcsb.org/pdb/files/2ncd.pdb "N" "L" "V" "D" "L" [,220] [,221] [,222] [,223] [,224] http://www.rcsb.org/pdb/files/1bg2.pdb "A" "G" "S" "E" "K" http://www.rcsb.org/pdb/files/1i6i.pdb "A" "G" "S" "E" "A" http://www.rcsb.org/pdb/files/1i5s.pdb "A" "G" "S" "E" "A" http://www.rcsb.org/pdb/files/2ncd.pdb "A" "G" "S" "E" "P" [,225] [,226] [,227] [,228] [,229] http://www.rcsb.org/pdb/files/1bg2.pdb "N" "I" "N" "K" "S" http://www.rcsb.org/pdb/files/1i6i.pdb "N" "I" "N" "K" "S" http://www.rcsb.org/pdb/files/1i5s.pdb "N" "I" "N" "K" "S" http://www.rcsb.org/pdb/files/2ncd.pdb "N" "I" "N" "R" "S" [,230] [,231] [,232] [,233] [,234] http://www.rcsb.org/pdb/files/1bg2.pdb "L" "S" "A" "L" "G" http://www.rcsb.org/pdb/files/1i6i.pdb "L" "T" "T" "L" "G" http://www.rcsb.org/pdb/files/1i5s.pdb "L" "T" "T" "L" "G" http://www.rcsb.org/pdb/files/2ncd.pdb "L" "S" "E" "L" "T" [,235] [,236] [,237] [,238] [,239] http://www.rcsb.org/pdb/files/1bg2.pdb "N" "V" "I" "S" "A" http://www.rcsb.org/pdb/files/1i6i.pdb "K" "V" "I" "S" "A" http://www.rcsb.org/pdb/files/1i5s.pdb "K" "V" "I" "S" "A" http://www.rcsb.org/pdb/files/2ncd.pdb "N" "V" "I" "L" "A" [,240] [,241] [,242] [,243] [,244] http://www.rcsb.org/pdb/files/1bg2.pdb "L" "A" "E" "G" "S" http://www.rcsb.org/pdb/files/1i6i.pdb "L" "A" "E" "M" "D" http://www.rcsb.org/pdb/files/1i5s.pdb "L" "A" "E" "M" "D" http://www.rcsb.org/pdb/files/2ncd.pdb "L" "L" "Q" "K" "Q" [,245] [,246] [,247] [,248] [,249] http://www.rcsb.org/pdb/files/1bg2.pdb "V" "P" "Y" "R" "D" http://www.rcsb.org/pdb/files/1i6i.pdb "I" "P" "Y" "R" "D" http://www.rcsb.org/pdb/files/1i5s.pdb "I" "P" "Y" "R" "D" http://www.rcsb.org/pdb/files/2ncd.pdb "I" "P" "Y" "R" "N" [,250] [,251] [,252] [,253] [,254] http://www.rcsb.org/pdb/files/1bg2.pdb "S" "K" "M" "T" "R" http://www.rcsb.org/pdb/files/1i6i.pdb "S" "V" "L" "T" "W" http://www.rcsb.org/pdb/files/1i5s.pdb "S" "V" "L" "T" "W" http://www.rcsb.org/pdb/files/2ncd.pdb "S" "K" "L" "T" "H" [,255] [,256] [,257] [,258] [,259] http://www.rcsb.org/pdb/files/1bg2.pdb "I" "L" "Q" "D" "S" http://www.rcsb.org/pdb/files/1i6i.pdb "L" "L" "R" "E" "N" http://www.rcsb.org/pdb/files/1i5s.pdb "L" "L" "R" "E" "N" http://www.rcsb.org/pdb/files/2ncd.pdb "L" "L" "M" "P" "S" [,260] [,261] [,262] [,263] [,264] http://www.rcsb.org/pdb/files/1bg2.pdb "L" "G" "G" "N" "C" http://www.rcsb.org/pdb/files/1i6i.pdb "L" "G" "G" "N" "S" http://www.rcsb.org/pdb/files/1i5s.pdb "L" "G" "G" "N" "S" http://www.rcsb.org/pdb/files/2ncd.pdb "L" "G" "G" "N" "S" [,265] [,266] [,267] [,268] [,269] http://www.rcsb.org/pdb/files/1bg2.pdb "R" "T" "T" "I" "V" http://www.rcsb.org/pdb/files/1i6i.pdb "R" "T" "A" "M" "V" http://www.rcsb.org/pdb/files/1i5s.pdb "R" "T" "A" "M" "V" http://www.rcsb.org/pdb/files/2ncd.pdb "K" "T" "L" "M" "F" [,270] [,271] [,272] [,273] [,274] http://www.rcsb.org/pdb/files/1bg2.pdb "I" "C" "C" "S" "P" http://www.rcsb.org/pdb/files/1i6i.pdb "A" "A" "L" "S" "P" http://www.rcsb.org/pdb/files/1i5s.pdb "A" "A" "L" "S" "P" http://www.rcsb.org/pdb/files/2ncd.pdb "I" "N" "V" "S" "P" [,275] [,276] [,277] [,278] [,279] http://www.rcsb.org/pdb/files/1bg2.pdb "S" "S" "Y" "N" "E" http://www.rcsb.org/pdb/files/1i6i.pdb "A" "D" "I" "N" "Y" http://www.rcsb.org/pdb/files/1i5s.pdb "A" "D" "I" "N" "Y" http://www.rcsb.org/pdb/files/2ncd.pdb "F" "Q" "D" "C" "F" [,280] [,281] [,282] [,283] [,284] http://www.rcsb.org/pdb/files/1bg2.pdb "S" "E" "T" "K" "S" http://www.rcsb.org/pdb/files/1i6i.pdb "D" "E" "T" "L" "S" http://www.rcsb.org/pdb/files/1i5s.pdb "D" "E" "T" "L" "S" http://www.rcsb.org/pdb/files/2ncd.pdb "Q" "E" "S" "V" "K" [,285] [,286] [,287] [,288] [,289] http://www.rcsb.org/pdb/files/1bg2.pdb "T" "L" "L" "F" "G" http://www.rcsb.org/pdb/files/1i6i.pdb "T" "L" "R" "Y" "A" http://www.rcsb.org/pdb/files/1i5s.pdb "T" "L" "R" "Y" "A" http://www.rcsb.org/pdb/files/2ncd.pdb "S" "L" "R" "F" "A" [,290] [,291] [,292] [,293] http://www.rcsb.org/pdb/files/1bg2.pdb "Q" "R" "A" "K" http://www.rcsb.org/pdb/files/1i6i.pdb "D" "R" "A" "K" http://www.rcsb.org/pdb/files/1i5s.pdb "D" "R" "A" "K" http://www.rcsb.org/pdb/files/2ncd.pdb "A" "S" "V" "N"##- 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" )Note: Accessing on-line PDB fileseq2aln(pdbseq(pdb), xaln, id = "1mkj")1 . . . . 50 [Truncated_Name:1]1bg2.pdb ------NIKVMCRFRPLNESEVNRGDKYIAKFQGEDTVXXXXVIASKXXX [Truncated_Name:2]1i6i.pdb ------SVKVAVRVRPFNSREMSRDSKCIIQMSGSTTTXXXXIVNPKQPK [Truncated_Name:3]1i5s.pdb ------SVKVAVRVRPFNSREMSRDSKCIIQMSGSTTTXXXXIVNPKQPK [Truncated_Name:4]2ncd.pdb ------NIRVFCRIRPPLESEENRMCXCTWTYHDESTVELQSIDAQAKSK [Truncated_Name:5]1mkj ADLAECNIKVMCRFRPLNESEVNRGDKYIAKFQGEDTVVIAS-------- ^^* * ** * * * 1 . . . . 50 51 . . . . 100 [Truncated_Name:1]1bg2.pdb XXXXPYAFDRVFQSSXXXXXXXXTSQEQVYNDCAKKIVKDVLEGYNGTIF [Truncated_Name:2]1i6i.pdb ETPKSFSFDYSYWSHTSPEDINYASQKQVYRDIGEEMLQHAFEGYNVCIF [Truncated_Name:3]1i5s.pdb ETPKSFSFDYSYWSHTSPEDINYASQKQVYRDIGEEMLQHAFEGYNVCIF [Truncated_Name:4]2ncd.pdb MGQQIFSFDQVFHPLXXXXXXXXSSQSDIFXEMVSPLIQSALDGYNICIF [Truncated_Name:5]1mkj ---KPYAFDRVFQSSTSQEQV--------YNDCAKKIVKDVLEGYNGTIF ^ ** ^ ^ ^ ^^ ^*** ** 51 . . . . 100 101 . . . . 150 [Truncated_Name:1]1bg2.pdb AYGQTSSGKTHTMEGKLHDPEGMGIIPRIVQDIFNYIYSMDENLXEFHIK [Truncated_Name:2]1i6i.pdb AYGQTGAGKSYTMMGKQEKXDQQGIIPQLCEDLFSRINDTTNDNMSYSVE [Truncated_Name:3]1i5s.pdb AYGQTGAGKSYTMMGKQEKXDQQGIIPQLCEDLFSRINDTTNDNMSYSVE [Truncated_Name:4]2ncd.pdb AYGQTGSGKTYTMDGVXXXPESVGVIPRTVDLLFDSIRGYRNLGWEYEIK [Truncated_Name:5]1mkj AYGQTSSGKTHTMEGKLHDPEGMGIIPRIVQDIFNYIYSMDEN-LEFHIK ***** **^ ** * ^ *^** ^* * ^ ^ 101 . . . . 150 151 . . . . 200 [Truncated_Name:1]1bg2.pdb VSYFEIYLDKIRDLLXDVSKTXNLSVHEDKNRVPYVKGCTERFVCSPDEV [Truncated_Name:2]1i6i.pdb VSYMEIYCERVRDLLXNPKNKGNLRVREHPLLGPYVEDLSKLAVTSYNDI [Truncated_Name:3]1i5s.pdb VSYMEIYCERVRDLLXNPKNKGNLRVREHPLLGPYVEDLSKLAVTSYNDI [Truncated_Name:4]2ncd.pdb ATFLEIYNEVLYDLLSNEQKDMEIRMAKNNKNDIYVSNITEETVLDPNHL [Truncated_Name:5]1mkj VSYFEIYLDKIRDLLD--VSKTNLSVHEDKNRVPYVKGCTERFVCSPDEV ^^ *** ^ ^ *** ^ ^ ** ^ * ^ 151 . . . . 200 201 . . . . 250 [Truncated_Name:1]1bg2.pdb MDTIDEGKSNRHVAVTNMNEHSSRSHSIFLINVKQENTQTXXXXEQKLSG [Truncated_Name:2]1i6i.pdb QDLMDSGNKARTVAATNMNETSSRSHAVFNIIFTQKRHDAETNITTEKVS [Truncated_Name:3]1i5s.pdb QDLMDSGNKARTVAATNMNETSSRSHAVFNIIFTQKRHDAETNITTEKVS [Truncated_Name:4]2ncd.pdb RHLMHTAKMNRATASTAGNERSSRSHAVTKLELIGRHAEKXXXXQEISVG [Truncated_Name:5]1mkj MDTIDEGKSNRHVAVTNMNEHSSRSHSIFLINVKQENTQTEQKLS----G ^ ^ * * * ** ***** ^ ^ 201 . . . . 250 251 . . . . 300 [Truncated_Name:1]1bg2.pdb KLYLVDLAGSEKVSKTGAEGAVLDEAKNINKSLSALGNVISALAEGSTYV [Truncated_Name:2]1i6i.pdb KISLVDLAGSEXXXXXXXXXXXXXXXANINKSLTTLGKVISALAEMDXFI [Truncated_Name:3]1i5s.pdb KISLVDLAGSERXXXXXAKGTRLKEGANINKSLTTLGKVISALAEMDXXI [Truncated_Name:4]2ncd.pdb SINLVDLAGSESXXXXXXXXXXXXXXPNINRSLSELTNVILALLQKQDHI [Truncated_Name:5]1mkj KLYLVDLAGSEKVAK------------NINKSLSALGNVISALAEGSTYV ^ ******** ***^**^ * ** ** ^ 251 . . . . 300 301 . . . . 350 [Truncated_Name:1]1bg2.pdb PYRDSKMTRILQDSLGGNCRTTIVICCSPSSYNESETKSTLLFGQRAKTI [Truncated_Name:2]1i6i.pdb PYRDSVLTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADRAKQI [Truncated_Name:3]1i5s.pdb PYRDSVLTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADRAKXX [Truncated_Name:4]2ncd.pdb PYRNSKLTHLLMPSLGGNSKTLMFINVSPFQDCFQESVKSLRFAASVNSC [Truncated_Name:5]1mkj PYRDSKMTRILQDSLGGNCRTTIVICCSPSSYNESETKSTLLFGQRAKTI *** * ^* ^* **** ^* ^ ** *^ ^* ^^ 301 . . . . 350 351 . . 374 [Truncated_Name:1]1bg2.pdb ------------------------ [Truncated_Name:2]1i6i.pdb ------------------------ [Truncated_Name:3]1i5s.pdb ------------------------ [Truncated_Name:4]2ncd.pdb ------------------------ [Truncated_Name:5]1mkj KNTVCVNVELTAEQWKKKYEKEKE 351 . . 374 Call: seq2aln(seq2add = pdbseq(pdb), aln = xaln, id = "1mkj") Class: fasta Alignment dimensions: 5 sequence rows; 374 position columns (306 non-gap, 68 gap) + attr: id, ali, call