Bio::SeqUtils(3)

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.