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Bio::Tools::Run::Alignment::Clustalw.3pm

NAME

Bio::Tools::Run::Alignment::Clustalw - Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Clustalw program

SYNOPSIS

   #  Build a clustalw alignment factory
   @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
   $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
 
   #  Pass the factory a list of sequences to be aligned.        
   $inputfilename = 't/data/cysprot.fa';
   $aln = $factory->align($inputfilename); # $aln is a SimpleAlign object.
   # or
   $seq_array_ref = \@seq_array;
   # where @seq_array is an array of Bio::Seq objects
   $aln = $factory->align($seq_array_ref);
 
   # Or one can pass the factory a pair of (sub)alignments
   #to be aligned against each other, e.g.:
   $aln = $factory->profile_align($aln1,$aln2);
   # where $aln1 and $aln2 are Bio::SimpleAlign objects.
 
   # Or one can pass the factory an alignment and one or more unaligned
   # sequences to be added to the alignment. For example:        
   $aln = $factory->profile_align($aln1,$seq); # $seq is a Bio::Seq object.
 
   # There are various additional options and input formats available.
   # See the DESCRIPTION section that follows for additional details.
 
 

DESCRIPTION

Note: this DESCRIPTION only documents the Bioperl interface to Clustalw. Clustalw, itself, is a large & complex program - for more information regarding clustalw, please see the clustalw documentation which accompanies the clustalw distribution. Clustalw is available from (among others) ftp://ftp.ebi.ac.uk/pub/software/. Clustalw.pm has only been tested using version 1.8 of clustalw. Compatibility with earlier versions of the clustalw program is currently unknown. Before running Clustalw successfully it will be necessary: to install clustalw on your system, and to ensure that users have execute privileges for the clustalw program.

Helping the module find your executable

You will need to enable Clustalw to find the clustalw program. This can be done in (at least) three ways:

  1. Make sure the clustalw executable is in your path so that
     which clustalw
     returns a clustalw executable on your system.
  2. Define an environmental variable CLUSTALDIR which is a 
     directory which contains the 'clustalw' application:
     In bash:
 
     export CLUSTALDIR=/home/username/clustalw1.8
 
     In csh/tcsh:
 
     setenv CLUSTALDIR /home/username/clustalw1.8
 
  3. Include a definition of an environmental variable CLUSTALDIR in
     every script that will use this Clustalw wrapper module, e.g.:
 
     BEGIN { $ENV{CLUSTALDIR} = '/home/username/clustalw1.8/' }
     use Bio::Tools::Run::Alignment::Clustalw;
 
 

If you are running an application on a webserver make sure the webserver environment has the proper PATH set or use the options 2 or 3 to set the variables.

How it works

Bio::Tools::Run::Alignment::Clustalw is an object for performing a multiple sequence alignment from a set of unaligned sequences and/or sub-alignments by means of the clustalw program.

Initially, a clustalw ``factory object'' is created. Optionally, the factory may be passed most of the parameters or switches of the clustalw program, e.g.:

         @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
         $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
 
 

Any parameters not explicitly set will remain as the defaults of the clustalw program. Additional parameters and switches (not available in clustalw) may also be set. Currently, the only such parameter is ``quiet'', which when set to a non-zero value, suppresses clustalw terminal output. Not all clustalw parameters are supported at this stage.

By default, Clustalw output is returned solely in a the form of a BioPerl Bio::SimpleAlign object which can then be printed and/or saved in multiple formats using the AlignIO.pm module. Optionally the raw clustalw output file can be saved if the calling script specifies an output file (with the clustalw parameter OUTFILE). Currently only the GCG-MSF output file formats is supported.

Other parameters and features (such as those corresponding to tree production) have not been implemented yet in Perl format.

Alignment parameters can be changed and/or examined at any time after the factory has been created. The program checks that any parameter/switch being set/read is valid. However, currently no additional checks are included to check that parameters are of the proper type (eg string or numeric) or that their values are within the proper range. As an example, to change the value of the clustalw parameter ktuple to 3 and subsequently to check its value one would write:

         $ktuple = 3;
         $factory->ktuple($ktuple);
         $get_ktuple = $factory->ktuple();
 
 

Once the factory has been created and the appropriate parameters set, one can call the method align() to align a set of unaligned sequences, or call profile_align() to add one or more sequences or a second alignment to an initial alignment.

Input to align() may consist of a set of unaligned sequences in the form of the name of file containing the sequences. For example,

   $inputfilename = 't/data/cysprot.fa'; 
   $aln = $factory-E<gt>align($inputfilename);
 
 

Alternately one can create an array of Bio::Seq objects somehow

         $str = Bio::SeqIO->new(-file=> 't/data/cysprot.fa', -format => 'Fasta');
         @seq_array =();
         while ( my $seq = $str->next_seq() ) {push (@seq_array, $seq) ;}
 
 

and pass the factory a reference to that array

         $seq_array_ref = \@seq_array;
         $aln = $factory->align($seq_array_ref);
 
 

In either case, align() returns a reference to a SimpleAlign object which can then used (see Bio::SimpleAlign).

Once an initial alignment exists, one can pass the factory additional sequence(s) to be added (ie aligned) to the original alignment. The alignment can be passed as either an alignment file or a Bio:SimpleAlign object. The unaligned sequence(s) can be passed as a filename or as an array of BioPerl sequence objects or as a single BioPerl Seq object. For example (to add a single sequence to an alignment),

         $str = Bio::AlignIO->new(-file=> 't/data/cysprot1a.msf');
         $aln = $str->next_aln();
         $str1 = Bio::SeqIO->new(-file=> 't/data/cysprot1b.fa');
         $seq = $str1->next_seq();
         $aln = $factory->profile_align($aln,$seq);
 
 

In either case, profile_align() returns a reference to a SimpleAlign object containing a new SimpleAlign object of the alignment with the additional sequence(s) added in.

Finally one can pass the factory a pair of (sub)alignments to be aligned against each other. The alignments can be passed in the form of either a pair of alignment files or a pair of Bio:SimpleAlign objects. For example,

         $profile1 = 't/data/cysprot1a.msf';
         $profile2 = 't/data/cysprot1b.msf';
         $aln = $factory->profile_align($profile1,$profile2);
 
 

or

         $str1 = Bio::AlignIO->new(-file=> 't/data/cysprot1a.msf');
         $aln1 = $str1->next_aln();
         $str2 = Bio::AlignIO->new(-file=> 't/data/cysprot1b.msf');
         $aln2 = $str2->next_aln();
         $aln = $factory->profile_align($aln1,$aln2);
 
 

In either case, profile_align() returns a reference to a SimpleAlign object containing an (super)alignment of the two input alignments.

For more examples of syntax and use of Clustalw, the user is encouraged to look at the script Clustalw.t in the t/ directory.

Note: Clustalw is still under development. Various features of the clustalw program have not yet been implemented. If you would like that a specific clustalw feature be added to this perl contact bioperl-l@bioperl.org.

These can be specified as paramters when instantiating a new Clustalw object, or through get/set methods of the same name (lowercase).

PARAMETER FOR ALIGNMENT COMPUTATION

KTUPLE

  Title       : KTUPLE
  Description : (optional) set the word size to be used in the alignment
                This is the size of exactly matching fragment that is used.
                INCREASE for speed (max= 2 for proteins; 4 for DNA),
                DECREASE for sensitivity.
                For longer sequences (e.g. >1000 residues) you may
                need to increase the default
 
 

TOPDIAGS

  Title       : TOPDIAGS
  Description : (optional) number of best diagonals to use
                The number of k-tuple matches on each diagonal
                (in an imaginary dot-matrix plot) is calculated.
                Only the best ones (with most matches) are used in
                the alignment.  This parameter specifies how many.
                Decrease for speed; increase for sensitivity.
 
 

WINDOW

  Title       : WINDOW
  Description : (optional) window size
                This is the number of diagonals around each of the 'best'
                diagonals that will be used.  Decrease for speed;
                increase for sensitivity.
 
 

PAIRGAP

  Title       : PAIRGAP
  Description : (optional) gap penalty for pairwise alignments
                This is a penalty for each gap in the fast alignments.
                It has little affect on the speed or sensitivity except
                for extreme values.
 
 

FIXEDGAP

  Title       : FIXEDGAP
  Description : (optional) fixed length gap penalty
 
 

FLOATGAP

  Title       : FLOATGAP
  Description : (optional) variable length gap penalty
 
 

MATRIX

  Title       : MATRIX
  Default     : PAM100 for DNA - PAM250 for protein alignment
  Description : (optional) substitution matrix used in the multiple
                alignments. Depends on the version of clustalw as to
                what default matrix will be used
 
                PROTEIN WEIGHT MATRIX leads to a new menu where you are
                offered a choice of weight matrices. The default for
                proteins in version 1.8 is the PAM series derived by
                Gonnet and colleagues. Note, a series is used! The
                actual matrix that is used depends on how similar the
                sequences to be aligned at this alignment step
                are. Different matrices work differently at each
                evolutionary distance.
 
                DNA WEIGHT MATRIX leads to a new menu where a single
                matrix (not a series) can be selected. The default is
                the matrix used by BESTFIT for comparison of nucleic
                acid sequences.
 
 

TYPE

  Title       : TYPE
  Description : (optional) sequence type: protein or DNA. This allows
                you to explicitly overide the programs attempt at
                guessing the type of the sequence.  It is only useful
                if you are using sequences with a VERY strange
                composition.
 
 

OUTPUT

  Title       : OUTPUT
  Description : (optional) clustalw supports GCG or PHYLIP or PIR or
                 Clustal format.  See the Bio::AlignIO modules for
                 which formats are supported by bioperl.
 
 

OUTFILE

  Title       : OUTFILE
  Description : (optional) Name of clustalw output file. If not set
                module will erase output file.  In any case alignment will
                be returned in the form of SimpleAlign objects
 
 

TRANSMIT

  Title       : TRANSMIT
  Description : (optional) transitions not weighted.  The default is to
                weight transitions as more favourable than other
                mismatches in DNA alignments.  This switch makes all
                nucleotide mismatches equally weighted.
 
 

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

   http://bugzilla.open-bio.org/
 
 

AUTHOR - Peter Schattner

Email schattner@alum.mit.edu

CONTRIBUTORS

Jason Stajich jason-AT-bioperl_DOT_org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

program_name

  Title   : program_name
  Usage   : $factory>program_name()
  Function: holds the program name
  Returns:  string
  Args    : None
 
 

program_dir

  Title   : program_dir
  Usage   : $factory->program_dir(@params)
  Function: returns the program directory, obtiained from ENV variable.
  Returns:  string
  Args    :
 
 

version

  Title   : version
  Usage   : exit if $prog->version() < 1.8
  Function: Determine the version number of the program
  Example :
  Returns : float or undef
  Args    : none
 
 

align

  Title   : align
  Usage   :
         $inputfilename = 't/data/cysprot.fa';
         $aln = $factory->align($inputfilename);
 or
         $seq_array_ref = \@seq_array; @seq_array is array of Seq objs
         $aln = $factory->align($seq_array_ref);
  Function: Perform a multiple sequence alignment
  Example :
  Returns : Reference to a SimpleAlign object containing the
            sequence alignment.
  Args    : Name of a file containing a set of unaligned fasta sequences
            or else an array of references to Bio::Seq objects.
 
  Throws an exception if argument is not either a string (eg a
  filename) or a reference to an array of Bio::Seq objects.  If
  argument is string, throws exception if file corresponding to string
  name can not be found. If argument is Bio::Seq array, throws
  exception if less than two sequence objects are in array.
 
 

profile_align

  Title   : profile_align
  Usage   :
  Function: Perform an alignment of 2 (sub)alignments
  Example :
  Returns : Reference to a SimpleAlign object containing the (super)alignment.
  Args    : Names of 2 files containing the subalignments
          or references to 2 Bio::SimpleAlign objects.
 
 

Throws an exception if arguments are not either strings (eg filenames) or references to SimpleAlign objects.

tree

  Title   : tree
  Usage   :
     @params = ('bootstrap' => 1000, 
                'tossgaps'  => 1, 
                'kimura'    => 1, 
                'seed'      => 121, 
                'bootlabels'=> 'nodes', 
                'quiet'     => 1);
     $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
     $tree_obj = $factory->tree($aln_obj);
 or
     $tree_obj = $factory->tree($treefilename);
  Function: 
  Returns : Bio::TreeIO object
  Args    :
 
 

_run

  Title   :  _run
  Usage   :  Internal function, not to be called directly        
  Function:   makes actual system call to clustalw program
  Example :
  Returns : nothing; clustalw output is written to a
            temporary file 
  Args    : Name of a file containing a set of unaligned fasta sequences
            and hash of parameters to be passed to clustalw
 
 

_setinput()

  Title   :  _setinput
  Usage   :  Internal function, not to be called directly        
  Function:   Create input file for clustalw program
  Example :
  Returns : name of file containing clustalw data input
  Args    : Seq or Align object reference or input file name
 
 

_setparams()

  Title   :  _setparams
  Usage   :  Internal function, not to be called directly        
  Function:   Create parameter inputs for clustalw program
  Example :
  Returns : parameter string to be passed to clustalw
            during align or profile_align
  Args    : name of calling object