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);
    my $catseq=$seqs[0];

    # 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);

    # simulate cloning of a fragment into a vector. Cut the vector at
    # positions 1000 and 1100 (deleting positions 1001 to 1099) and
    # "ligate" a fragment into the sites. The fragment is
    # reverse-complemented in this example (option "flip"). 
    # All features of the vector and fragment are preserved and 
    # features that are affected by the deletion/insertion are 
    # modified accordingly.
    # $vector and $fragment must be Bio::SeqI compliant objects 
    my $new_molecule = Bio::Sequtils->ligate(
      -vector => $vector, 
      -fragment => $fragment,
      -left => 1000,
      -right => 1100,
      -flip => 1 
    );

    # delete a segment of a sequence (from pos 1000 to 1100, inclusive),
    # again preserving features and annotations
    my $new_molecule = Bio::SeqUtils->cut( $seq, 1000, 1100 );

    # insert a fragment into a recipient between positions 1000 and
    # 1001. $recipient is a Bio::SeqI compliant object
    my $new_molecule =  Bio::SeqUtils::PbrTools->insert( 
      $recipient_seq, 
      $fragment_seq,
      1000
    );

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.

There are also methods that simulate molecular cloning with rich sequence objects. The delete() method cuts a segment out of a sequence and re-joins the left and right fragments (like splicing or digesting and re-ligating a molecule). Positions (and types) of sequence features are adjusted accordingly: Features that span the deleted segment are converted to split featuress to indicate the disruption. (Sub)Features that extend into the deleted segment are truncated. A new molecule is created and returned.

The insert() method inserts a fragment (which can be a rich Bio::Seq object) into another sequence object adding all annotations and features to the final product. Features that span the insertion site are converted to split features to indicate the disruption. A new feature is added to indicate the inserted fragment itself. A new molecule is created and returned.

The ligate() method simulates digesting a recipient (vector) and ligating a fragment into it, which can also be flipped if needed. It is simply a combination of a deletion and an insertion step and returns a new molecule. The rules for modifying feature locations outlined above are also used here, e.g. features that span the cut sites are converted to split features with truncated sub-locations.

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:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Heikki Lehvaslaiho

Email: heikki-at-bioperl-dot-org

CONTRIBUTORS

Roy R. Chaudhuri - roy.chaudhuri at gmail.com Frank Schwach - frank.schwach@sanger.ac.uk

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   : Bio::SeqUtils->cat(@seqs);
            my $catseq=$seqs[0];
  Function: Concatenates a list of Bio::Seq objects, adding them all on to the
            end of the first sequence. Annotations and sequence features are
            copied over from any additional objects, and the coordinates of any
            copied features are adjusted appropriately.
  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)

delete

 Title   : delete
 Function: cuts a segment out of a sequence and re-joins the left and right fragments
           (like splicing or digesting and re-ligating a molecule).
           Positions (and types) of sequence features are adjusted accordingly:
           Features that span the cut site are converted to split featuress to
           indicate the disruption. 
           Features that extend into the cut-out fragment are truncated.
           A new molecule is created and returned.
 Usage   : my $cutseq =  Bio::SeqUtils::PbrTools->cut( $seq, 1000, 1100 );
 Args    : a Bio::PrimarySeqI compliant object to cut,
           first nt of the segment to be deleted 
           last nt of the segment to be deleted  
           optional:
           hash-ref of options:
            clone_obj: if true, clone the input sequence object rather
                       than calling "new" on the object's class 

 Returns : a new Bio::Seq object

insert

 Title   : insert
 Function: inserts a fragment (a Bio::Seq object) into a nother sequence object
           adding all annotations and features to the final product.
           Features that span the insertion site are converted to split
           features to indicate the disruption.
           A new feature is added to indicate the inserted fragment itself.
           A new molecule is created and returned.
 Usage   : # insert a fragment after pos 1000
           my $insert_seq =  Bio::SeqUtils::PbrTools->insert( 
             $recipient_seq, 
             $fragment_seq,
             1000
           );
 Args    : recipient sequence (a Bio::PrimarySeqI compliant object),
           a fragmetn to insert (Bio::PrimarySeqI compliant object), 
           insertion position (fragment is inserted to the right of this pos)
            pos=0 will prepend the fragment to the recipient
           optional:
           hash-ref of options:
            clone_obj: if true, clone the input sequence object rather
                       than calling "new" on the object's class 
 Returns : a new Bio::Seq object

ligate

 title   : ligate
 function: pastes a fragment (which can also have features) into a recipient 
           sequence between two "cut" sites, preserving features and adjusting 
           their locations.
           This is a shortcut for deleting a segment from a sequence object followed
           by an insertion of a fragmnet and is supposed to be used to simulate
           in-vitro cloning where a recipient (a vector) is digested and a fragment 
           is then ligated into the recipient molecule. The fragment can be flipped
           (reverse-complemented with all its features).
           A new sequence object is returned to represent the product of the reaction.
           Features and annotations are transferred from the insert to the product
           and features on the recipient are adjusted according to the methods 
           L</"delete"> amd L</"insert">:
           Features spanning the insertion site will be split up into two sub-locations.
           (Sub-)features in the deleted region are themselves deleted.
           (Sub-)features that extend into the deleted region are truncated. 
           The class of the product object depends on the class of the recipient (vector)
           sequence object. if it is not possible to instantiate a new
           object of that class, a Bio::Primaryseq object is created instead.
 usage   : # insert the flipped fragment between positions 1000 and 1100 of the 
           # vector, i.e. everything between these two positions is deleted and
           # replaced by the fragment
           my $new_molecule = Bio::Sequtils::Pbrtools->ligate(
             -recipient => $vector, 
             -fragment => $fragment,
             -left => 1000,
             -right => 1100,
             -flip      => 1, 
             -clone_obj => 1 
           );
 args    : recipient: the recipient/vector molecule
           fragment: molecule that is to be ligated into the vector
           left: left cut site (fragment will be inserted to the right of 
                 this position)
           optional:
            right: right cut site (fragment will be inseterted to the 
                   left of this position). defaults to left+1
            flip: boolean, if true, the fragment is reverse-complemented 
                  (including features) before inserting
            clone_obj: if true, clone the recipient object to create the product
                       instead of calling "new" on its class
 returns : a new Bio::Seq object of the ligated fragments

_coord_adjust_deletion

 title   : _coord_adjust_deletion
 function: recursively adjusts coordinates of seqfeatures on a molecule
           where a segment has been deleted.
           (sub)features that span the deletion site become split features.
           (sub)features that extend into the deletion site are truncated.
           A note is added to the feature to inform about the size and
           position of the deletion.
 usage   : my $adjusted_feature = Bio::Sequtils::_coord_adjust_deletion( 
             $feature,
             $start,
             $end
           );
 args    : a Bio::SeqFeatureI compliant object,
           start (inclusive) position of the deletion site,
           end (inclusive) position of the deletion site
 returns : a Bio::SeqFeatureI compliant object

_coord_adjust_insertion

 title   : _coord_adjust_insertion
 function: recursively adjusts coordinates of seqfeatures on a molecule
           where another sequence has been inserted.
           (sub)features that span the insertion site become split features
           and a note is added about the size and positin of the insertion.
           Features with an IN-BETWEEN location at the insertion site
           are lost (such features can only exist between adjacent bases)
 usage   : my $adjusted_feature = Bio::Sequtils::_coord_adjust_insertion( 
             $feature,
             $insert_pos,
             $insert_length
           );
 args    : a Bio::SeqFeatureI compliant object,
           insertion position (insert to the right of this position)
           length of inserted fragment
 returns : a Bio::SeqFeatureI compliant object

_single_loc_object_from_collection

 Title   : _single_loc_object_from_collection
 Function: takes an array of location objects. Returns either a split 
           location object if there are more than one locations in the 
           array or returns the single location if there is only one
 Usage   : my $loc = _single_loc_object_from_collection( @sublocs );
 Args    : array of Bio::Location objects
 Returns : a single Bio:;Location object containing all locations

_location_objects_from_coordinate_list

 Title   : _location_objects_from_coordinate_list
 Function: takes an array-ref of start/end coordinates, a strand and a 
           type and returns a list of Bio::Location objects (Fuzzy by 
           default, Simple in case of in-between coordinates).
           If location type is not "IN-BETWEEN", individual types may be
           passed in for start and end location as per Bio::Location::Fuzzy
           documentation.
 Usage   : my @loc_objs = $self->_location_objects_from_coordinate_list( 
             \@coords, 
             $strand, 
             $type
           );
 Args    : array-ref of array-refs each containing:
           start, end [, start-type, end-type]   
             where types are optional. If given, must be
             a one of ('BEFORE', 'AFTER', 'EXACT','WITHIN', 'BETWEEN')
           strand (all locations must be on same strand)
           location-type (EXACT, IN-BETWEEN etc)
 Returns : list of Bio::Location objects

_new_seq_via_clone

 Title   : _new_seq_via_clone
 Function: clone a sequence object using Bio::Root::Root::clone and set the new sequence string
           sequence features are removed.
 Usage   : my $new_seq = $self->_new_seq_via_clone( $seq_obj, $seq_str );
 Args    : original seq object [, new sequence string]
 Returns : a clone of the original sequence object, optionally with new sequence string

_new_seq_from_old

 Title   : _new_seq_from_old
 Function: creates a new sequence obejct, if possible of the same class as the old and adds 
           attributes to it. Also copies annotation across to the new object.
 Usage   : my $new_seq = $self->_new_seq_from_old( $seq_obj, { seq => $seq_str, display_id => 'some_ID'});
 Args    : old sequence object
           hashref of attributes for the new sequence (sequence string etc.)
 Returns : a new Bio::Seq object

_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.