Printing Sequence Alignments

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)