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Bio::SeqUtils.3pm

NAME

Bio::SeqUtils - Additional methods for PrimarySeq objects

SYNOPSIS

     use Bio::SeqUtils;
     # get a Bio::PrimarySeqI compliant object, $seq, somehow
     $util = Bio::SeqUtils->new();
     $polypeptide_3char = $util->seq3($seq);
     # or
     $polypeptide_3char = Bio::SeqUtils->seq3($seq);
 
     # set the sequence string (stored in one char code in the object)
     Bio::SeqUtils->seq3($seq, $polypeptide_3char);
 
     # translate a sequence in all six frames
     @seqs = Bio::SeqUtils->translate_6frames($seq);
 
     # inplace editing of the sequence
     Bio::SeqUtils->mutate($seq,
                           Bio::LiveSeq::Mutation->new(-seq => 'c',
                                                       -pos => 3
                                                      ));
     # mutate a sequence to desired similarity%
     $newseq = Bio::SeqUtils-> evolve
         ($seq, $similarity, $transition_transversion_rate);
 
 
     # concatenate two or more sequences with annotations and features,
     # the first sequence will be modified
     Bio::SeqUtils->cat(@seqs);
 
     # truncate a sequence, retaining features and adjusting their
     # coordinates if necessary
     my $truncseq = Bio::SeqUtils->trunc_with_features($seq, 100, 200);
 
     # reverse complement a sequence and its features
     my $revcomseq = Bio::SeqUtils->revcom_with_features($seq);
 
 

DESCRIPTION

This class is a holder of methods that work on Bio::PrimarySeqI- compliant sequence objects, e.g. Bio::PrimarySeq and Bio::Seq. These methods are not part of the Bio::PrimarySeqI interface and should in general not be essential to the primary function of sequence objects. If you are thinking of adding essential functions, it might be better to create your own sequence class. See Bio::PrimarySeqI, Bio::PrimarySeq, and Bio::Seq for more.

The methods take as their first argument a sequence object. It is possible to use methods without first creating a SeqUtils object, i.e. use it as an anonymous hash.

The first two methods, seq3() and seq3in(), give out or read in protein sequences coded in three letter IUPAC amino acid codes.

The next two methods, translate_3frames() and translate_6frames(), wrap around the standard translate method to give back an array of three forward or all six frame translations.

The mutate() method mutates the sequence string with a mutation description object.

The cat() method concatenates two or more sequences. The first sequence is modified by addition of the remaining sequences. All annotations and sequence features will be transferred.

The revcom_with_features() and trunc_with_features() methods are similar to the revcom() and trunc() methods from Bio::Seq, but also adjust any features associated with the sequence as appropriate.

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://bugzilla.open-bio.org/
 
 

AUTHOR - Heikki Lehvaslaiho

Email: heikki-at-bioperl-dot-org

CONTRIBUTORS

Roy R. Chaudhuri - roy.chaudhuri at gmail.com

APPENDIX

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

seq3

  Title   : seq3
  Usage   : $string = Bio::SeqUtils->seq3($seq)
  Function: Read only method that returns the amino acid sequence as a
            string of three letter codes. alphabet has to be
            'protein'. Output follows the IUPAC standard plus 'Ter' for
            terminator. Any unknown character, including the default
            unknown character 'X', is changed into 'Xaa'. A noncoded
            aminoacid selenocystein is recognized (Sec, U).
 
  Returns : A scalar
  Args    : character used for stop in the protein sequence optional,
            defaults to '*' string used to separate the output amino
            acid codes, optional, defaults to ''
 
 

seq3in

  Title   : seq3in
  Usage   : $seq = Bio::SeqUtils->seq3in($seq, 'MetGlyTer')
  Function: Method for changing of the sequence of a
            Bio::PrimarySeqI sequence object. The three letter amino
            acid input string is converted into one letter code.  Any
            unknown character triplet, including the default 'Xaa', is
            converted into 'X'.
 
  Returns : Bio::PrimarySeq object
  Args    : sequence string
            optional character to be used for stop in the protein sequence,
               defaults to '*'
            optional character to be used for unknown in the protein sequence,
               defaults to 'X'
 
 

translate_3frames

  Title   : translate_3frames
  Usage   : @prots = Bio::SeqUtils->translate_3frames($seq)
  Function: Translate a nucleotide sequence in three forward frames.
            The IDs of the sequences are appended with '-0F', '-1F', '-2F'.
  Returns : An array of seq objects
  Args    : sequence object
            same arguments as to Bio::PrimarySeqI::translate
 
 

translate_6frames

  Title   : translate_6frames
  Usage   : @prots = Bio::SeqUtils->translate_6frames($seq)
  Function: translate a nucleotide sequence in all six frames
            The IDs of the sequences are appended with '-0F', '-1F', '-2F',
            '-0R', '-1R', '-2R'.
  Returns : An array of seq objects
  Args    : sequence object
            same arguments as to Bio::PrimarySeqI::translate
 
 

valid_aa

  Title   : valid_aa
  Usage   : my @aa = $table->valid_aa
  Function: Retrieves a list of the valid amino acid codes.
            The list is ordered so that first 21 codes are for unique 
            amino acids. The rest are ['B', 'Z', 'X', '*'].
  Returns : array of all the valid amino acid codes
  Args    : [optional] $code => [0 -> return list of 1 letter aa codes,
                                 1 -> return list of 3 letter aa codes,
                                 2 -> return associative array of both ]
 
 

mutate

  Title   : mutate
  Usage   : Bio::SeqUtils->mutate($seq,$mutation1, $mutation2);
  Function: Inplace editing of the sequence.
 
            The second argument can be a Bio::LiveSeq::Mutation object
            or an array of them. The mutations are applied sequentially
            checking only that their position is within the current
            sequence.  Insertions are inserted before the given
            position.
 
  Returns : boolean
  Args    : sequence object
            mutation, a Bio::LiveSeq::Mutation object, or an array of them
 
 

See Bio::LiveSeq::Mutation.

cat

   Title   : cat
   Usage   : my $catseq = Bio::SeqUtils->cat(@seqs)
   Function: Concatenates an array of Bio::Seq objects, using the first sequence
             as a target. Annotations and sequence features are copied over 
             from any additional objects. Adjusts the coordinates of copied 
             features.
   Returns : a boolean
   Args    : array of sequence objects
 
 

Note that annotations have no sequence locations. If you concatenate sequences with the same annotations they will all be added.

trunc_with_features

  Title   : trunc_with_features
  Usage   : $trunc=Bio::SeqUtils->trunc_with_features($seq, $start, $end);
  Function: Like Bio::Seq::trunc, but keeps features (adjusting coordinates
            where necessary. Features that partially overlap the region have
            their location changed to a Bio::Location::Fuzzy.
  Returns : A new sequence object
  Args    : A sequence object, start coordinate, end coordinate (inclusive)
 
 

_coord_adjust

   Title   : _coord_adjust
   Usage   : my $newfeat=Bio::SeqUtils->_coord_adjust($feature, 100, $seq->length);
   Function: Recursive subroutine to adjust the coordinates of a feature
             and all its subfeatures. If a sequence length is specified, then
             any adjusted features that have locations beyond the boundaries
             of the sequence are converted to Bio::Location::Fuzzy objects.
 
   Returns : A Bio::SeqFeatureI compliant object.
   Args    : A Bio::SeqFeatureI compliant object,
             the number of bases to add to the coordinates
             (optional) the length of the parent sequence
 
 

revcom_with_features

  Title   : revcom_with_features
  Usage   : $revcom=Bio::SeqUtils->revcom_with_features($seq);
  Function: Like Bio::Seq::revcom, but keeps features (adjusting coordinates
            as appropriate.
  Returns : A new sequence object
  Args    : A sequence object
 
 

_feature_revcom

   Title   : _feature_revcom
   Usage   : my $newfeat=Bio::SeqUtils->_feature_revcom($feature, $seq->length);
   Function: Recursive subroutine to reverse complement a feature and
             all its subfeatures. The length of the parent sequence must be
             specified.
 
   Returns : A Bio::SeqFeatureI compliant object.
   Args    : A Bio::SeqFeatureI compliant object,
             the length of the parent sequence
 
 

evolve

   Title   : evolve
   Usage   : my $newseq = Bio::SeqUtils->
                 evolve($seq, $similarity, $transition_transversion_rate);
   Function: Mutates the sequence by point mutations until the similarity of
             the new sequence has decreased to the required level. 
             Transition/transversion rate is adjustable.
   Returns : A new Bio::PrimarySeq object
   Args    : sequence object
             percentage similarity (e.g. 80)
             tr/tv rate, optional, defaults to 1 (= 1:1)
 
 

Set the verbosity of the Bio::SeqUtils object to positive integer to see the mutations as they happen.

This method works only on nucleotide sequences. It prints a warning if you set the target similarity to be less than 25%.

Transition/transversion ratio is an observed attribute of an sequence comparison. We are dealing here with the transition/transversion rate that we set for our model of sequence evolution.