Printing Sequence Alignments

Usage

"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’.

Description

Print method for fasta and pdbs sequence alignment objects.

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.

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)

See also

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

Author

Barry Grant