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.

# Get a tree of the sequences
$tree = $factory->tree(\@seq_array);

# Get both an alignment and a tree
($aln, $tree) = $factory->run(\@seq_array);

# Do a footprinting analysis on the supplied sequences, getting back the
# most conserved sub-alignments
my @results = $factory->footprint(\@seq_array);
foreach my $result (@results) {
  print $result->consensus_string, "\n";
}

# 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 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.

Not all parameters and features have 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);

$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 parameters 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

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Peter Schattner

Email schattner@alum.mit.edu

CONTRIBUTORS

Jason Stajich jason-AT-bioperl_DOT_org Sendu Bala bix@sendu.me.uk

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, obtained 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

run

Title   : run
Usage   : ($aln, $tree) = $factory->run($inputfilename);
          ($aln, $tree) = $factory->run($seq_array_ref);
Function: Perform a multiple sequence alignment, generating a tree at the same
          time. (Like align() and tree() combined.)
Returns : A SimpleAlign object containing the sequence alignment and a
          Bio::Tree::Tree object with the tree relating the sequences.
Args    : Name of a file containing a set of unaligned fasta sequences
          or else an array of references to Bio::Seq objects.

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
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   : $aln = $factory->profile_align(@simple_aligns);
          or
          $aln = $factory->profile_align(@subalignment_filenames);
Function: Perform an alignment of 2 (sub)alignments
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.

add_sequences

Title   : add_sequences
Usage   :
Function: Align and add sequences into an alignment
Example :
Returns : Reference to a SimpleAlign object containing the (super)alignment.
Args    : Names of 2 files, the first one containing an alignment and the second one containing sequences to be added
        or references to 2 Bio::SimpleAlign objects.