seq2aln. bio3d 2.3-0

Usage

seq2aln(seq2add, aln, id = "seq", file = "aln.fa", ...)

Arguments

seq2add: an sequence character vector or an alignment list object with id and ali components, similar to that generated by read.fasta and seqaln.
aln: an alignment list object with id and ali components, similar to that generated by read.fasta and seqaln.
id: a vector of sequence names to serve as sequence identifers.
file: name of ‘FASTA’ output file to which alignment should be written.
...: additional arguments passed to seqaln.

Description

Add one or more sequences to an existing multiple alignment that you wish to keep intact.

Details

This function calls the ‘MUSCLE’ program, to perform a profile profile alignment, which MUST BE INSTALLED on your system and in the search path for executables.

Value

ali: an alignment character matrix with a row per sequence and a column per equivalent aminoacid/nucleotide.
id: sequence names as identifers.

References

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

‘MUSCLE’ is the work of Edgar: Edgar (2004) Nuc. Acid. Res. 32, 1792--1797.

Full details of the ‘MUSCLE’ algorithm, along with download and installation instructions can be obtained from: http://www.drive5.com/muscle.

Note

A system call is made to the ‘MUSCLE’ program, which must be installed on your system and in the search path for executables.

Examples


aa.1 <- pdbseq( read.pdb("1bg2") )

  Note: Accessing on-line PDB file

aa.2 <- pdbseq( read.pdb("3dc4") )

  Note: Accessing on-line PDB file

aa.3 <- pdbseq( read.pdb("1mkj") )

  Note: Accessing on-line PDB file


aln <- seqaln( seqbind(aa.1,aa.2) )

seq2aln(aa.3, aln)

       1        .         .         .         .         .         .         70 
seq1   -DLAECNIKVMCRFRPLNESEVNRGDKYIAKFQGEDTVVIASKPYAFDRVFQSSTSQEQVYNDCAKKIVK
seq2   --AKLSAVRIAVREAPYRPSVVQ-----FPPWSDGKSLIVDQNEFHFDHAFPATISQDEMYQALILPLVD
seq    ADLAECNIKVMCRFRPLNESEVNRGDKYIAKFQGEDTVVIASKPYAFDRVFQSSTSQEQVYNDCAKKIVK
              ^^^  *  *   * *^        ^    ^^^^    ^ **^ *  ^ **^ ^*^     ^*  
       1        .         .         .         .         .         .         70 

      71        .         .         .         .         .         .         140 
seq1   DVLEGYNGTIFAYGQTSSGKTHTM----EGKLHDPEGMGIIPRIVQDIFNYIYSMDENLEFHIKV--SYF
seq2   KLLEGFQCTALAYGQTGTGKSYSMGMTPPGEIL-PEHLGILPRALGDIFERVTARQENNKDAIQVYASFI
seq    DVLEGYNGTIFAYGQTSSGKTHTM----EGKLHDPEGMGIIPRIVQDIFNYIYSMDENLEFHIKV--SYF
        ^***^^ *  ***** ^**^ ^*     * ^  ** ^**^** ^ ***  ^    **    * *  *^  
      71        .         .         .         .         .         .         140 

     141        .         .         .         .         .         .         210 
seq1   EIYLDKIRDLLDVSKTNLSVHEDKNRVPYVKGCTERFVCSPDEVMDTIDEGKSNRHVAVTNMNEHSSRSH
seq2   EIYNEKPFDLLGSTP----------HMPMVAARCQRCTCLP------LHSQADLHHILELGTRNRRSRSH
seq    EIYLDKIRDLLDVSKTNLSVHEDKNRVPYVKGCTERFVCSPDEVMDTIDEGKSNRHVAVTNMNEHSSRSH
       *** ^*  ***  ^           ^^* * ^   *  * *      ^      ^*^       ^ **** 
     141        .         .         .         .         .         .         210 

     211        .         .         .         .         .         .         280 
seq1   SIFLINVKQENTQTEQKLSGKLYLVDLAGSEKVSKTGAEGAVLDEAKNINKSLSALGNVISALAEGSTYV
seq2   AIVTIHVKSKTHHS------RMNIVDLAGSEGVV-------------NINLGLLSINKVVMSMAAGHTVI
seq    SIFLINVKQENTQTEQKLSGKLYLVDLAGSEKVA------------KNINKSLSALGNVISALAEGSTYV
        *  * **     ^      ^^ ^******* *              ***  *  ^  *^  ^* * * ^ 
     211        .         .         .         .         .         .         280 

     281        .         .         .         .         .         .         350 
seq1   PYRDSKMTRILQDSLGGNCRTTIVICCSPSSYNESETKSTLLFGQRAKTI--------------------
seq2   PYRDSVLTTVLQASLTAQSYLTFLACISPHQCDLSETLSTLRFGTSAKAAALEH----------------
seq    PYRDSKMTRILQDSLGGNCRTTIVICCSPSSYNESETKSTLLFGQRAKTIKNTVCVNVELTAEQWKKKYE
       ***** ^* ^** ** ^^   * ^ * **     *** *** **  **                       
     281        .         .         .         .         .         .         350 

     351  354 
seq1   ----
seq2   ----
seq    KEKE
            
     351  354 

Call:
  seq2aln(seq2add = aa.3, aln = aln)

Class:
  fasta

Alignment dimensions:
  3 sequence rows; 354 position columns (281 non-gap, 73 gap) 

+ attr: id, ali, call

Author

Barry Grant

Add a Sequence to an Existing Alignmnet