Print method for fasta and pdbs sequence alignment objects.

# S3 method for fasta
print(x, alignment=TRUE, ...)
.print.fasta.ali(x, width = NULL, col.inds = NULL, numbers = TRUE,
         conservation=TRUE, ...)

Arguments

x

a sequence alignment object as obtained from the functions read.fasta, read.fasta.pdb, pdbaln, seqaln, etc.

alignment

logical, if TRUE the sequence alignment will be printed to screen.

width

a single numeric value giving the number of residues per printed sequence block. By default this is determined from considering alignment identifier widths given a standard 85 column terminal window.

col.inds

an optional numeric vector that can be used to select subsets of alignment positions/columns for printing.

numbers

logical, if TRUE position numbers and a tick-mark every 10 positions are printed above and below sequence blocks.

conservation

logical, if TRUE conserved and semi-conserved columns in the alignment are marked with an ‘*’ and ‘^’, respectively.

...

additional arguments to ‘.print.fasta.ali’.

Value

Called mostly for its effect but also silently returns block divided concatenated sequence strings as a matrix.

References

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

Author

Barry Grant

See also

read.fasta, read.fasta.pdb, pdbaln, seqaln

Examples

file <- system.file("examples/kif1a.fa",package="bio3d") aln <- read.fasta(file) print(aln)
#> 1 . . . . 50 #> [Truncated_Name:1]1bg2.pdb NIKVMCRFRPLNESEVNRGDKYIAKFQGEDTV----VIASK-------PY #> [Truncated_Name:2]1i6i.pdb SVKVAVRVRPFNSREMSRDSKCIIQMSGSTTT----IVNPKQPKETPKSF #> [Truncated_Name:3]1i5s.pdb SVKVAVRVRPFNSREMSRDSKCIIQMSGSTTT----IVNPKQPKETPKSF #> [Truncated_Name:4]2ncd.pdb NIRVFCRIRPPLESEENRMC-CTWTYHDESTVELQSIDAQAKSKMGQQIF #> ^^* * ** * * * ^ ^ #> 1 . . . . 50 #> #> 51 . . . . 100 #> [Truncated_Name:1]1bg2.pdb AFDRVFQSS--------TSQEQVYNDCAKKIVKDVLEGYNGTIFAYGQTS #> [Truncated_Name:2]1i6i.pdb SFDYSYWSHTSPEDINYASQKQVYRDIGEEMLQHAFEGYNVCIFAYGQTG #> [Truncated_Name:3]1i5s.pdb SFDYSYWSHTSPEDINYASQKQVYRDIGEEMLQHAFEGYNVCIFAYGQTG #> [Truncated_Name:4]2ncd.pdb SFDQVFHPL--------SSQSDIF-EMVSPLIQSALDGYNICIFAYGQTG #> ** ^ ** ^^ ^ ^^ ^*** ******* #> 51 . . . . 100 #> #> 101 . . . . 150 #> [Truncated_Name:1]1bg2.pdb SGKTHTMEGKLHDPEGMGIIPRIVQDIFNYIYSMDENL-EFHIKVSYFEI #> [Truncated_Name:2]1i6i.pdb AGKSYTMMGKQEK-DQQGIIPQLCEDLFSRINDTTNDNMSYSVEVSYMEI #> [Truncated_Name:3]1i5s.pdb AGKSYTMMGKQEK-DQQGIIPQLCEDLFSRINDTTNDNMSYSVEVSYMEI #> [Truncated_Name:4]2ncd.pdb SGKTYTMDGV---PESVGVIPRTVDLLFDSIRGYRNLGWEYEIKATFLEI #> **^ ** * ^ *^** ^* * ^ ^ ^^ ** #> 101 . . . . 150 #> #> 151 . . . . 200 #> [Truncated_Name:1]1bg2.pdb YLDKIRDLL-DVSKT-NLSVHEDKNRVPYVKGCTERFVCSPDEVMDTIDE #> [Truncated_Name:2]1i6i.pdb YCERVRDLL-NPKNKGNLRVREHPLLGPYVEDLSKLAVTSYNDIQDLMDS #> [Truncated_Name:3]1i5s.pdb YCERVRDLL-NPKNKGNLRVREHPLLGPYVEDLSKLAVTSYNDIQDLMDS #> [Truncated_Name:4]2ncd.pdb YNEVLYDLLSNEQKDMEIRMAKNNKNDIYVSNITEETVLDPNHLRHLMHT #> * ^ ^ *** ^ ^ ** ^ * ^ ^ #> 151 . . . . 200 #> #> 201 . . . . 250 #> [Truncated_Name:1]1bg2.pdb GKSNRHVAVTNMNEHSSRSHSIFLINVKQENTQT----EQKLSGKLYLVD #> [Truncated_Name:2]1i6i.pdb GNKARTVAATNMNETSSRSHAVFNIIFTQKRHDAETNITTEKVSKISLVD #> [Truncated_Name:3]1i5s.pdb GNKARTVAATNMNETSSRSHAVFNIIFTQKRHDAETNITTEKVSKISLVD #> [Truncated_Name:4]2ncd.pdb AKMNRATASTAGNERSSRSHAVTKLELIGRHAEK----QEISVGSINLVD #> ^ * * * ** ***** ^ ^ ^ *** #> 201 . . . . 250 #> #> 251 . . . . 300 #> [Truncated_Name:1]1bg2.pdb LAGSEKVSKTGAEGAVLDEAKNINKSLSALGNVISALAEGSTYVPYRDSK #> [Truncated_Name:2]1i6i.pdb LAGSE---------------ANINKSLTTLGKVISALAEMD-FIPYRDSV #> [Truncated_Name:3]1i5s.pdb LAGSER-----AKGTRLKEGANINKSLTTLGKVISALAEMD--IPYRDSV #> [Truncated_Name:4]2ncd.pdb LAGSES--------------PNINRSLSELTNVILALLQKQDHIPYRNSK #> ***** ***^**^ * ** ** ^*** * #> 251 . . . . 300 #> #> 301 . . . . 344 #> [Truncated_Name:1]1bg2.pdb MTRILQDSLGGNCRTTIVICCSPSSYNESETKSTLLFGQRAKTI #> [Truncated_Name:2]1i6i.pdb LTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADRAKQI #> [Truncated_Name:3]1i5s.pdb LTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADRAK-- #> [Truncated_Name:4]2ncd.pdb LTHLLMPSLGGNSKTLMFINVSPFQDCFQESVKSLRFAASVNSC #> ^* ^* **** ^* ^ ** *^ ^* ^^ #> 301 . . . . 344 #> #> Call: #> read.fasta(file = file) #> #> Class: #> fasta #> #> Alignment dimensions: #> 4 sequence rows; 344 position columns (293 non-gap, 51 gap) #> #> + attr: id, ali, call
# print(aln, col.inds=30:100, numbers=FALSE)