/ 
FAST-1.06
River stage zero No dependents
/ FAST::Bio::SeqUtils

NAME

FAST::Bio::SeqUtils - Additional methods for PrimarySeq objects

SYNOPSIS

use FAST::Bio::SeqUtils;
# get a FAST::Bio::PrimarySeqI compliant object, $seq, somehow
$util = FAST::Bio::SeqUtils->new();
$polypeptide_3char = $util->seq3($seq);
# or
$polypeptide_3char = FAST::Bio::SeqUtils->seq3($seq);

# set the sequence string (stored in one char code in the object)
FAST::Bio::SeqUtils->seq3($seq, $polypeptide_3char);

# translate a sequence in all six frames
@seqs = FAST::Bio::SeqUtils->translate_6frames($seq);

# inplace editing of the sequence
FAST::Bio::SeqUtils->mutate($seq,
                      FAST::Bio::LiveSeq::Mutation->new(-seq => 'c',
                                                  -pos => 3
                                                 ));
# mutate a sequence to desired similarity%
$newseq = FAST::Bio::SeqUtils-> evolve
    ($seq, $similarity, $transition_transversion_rate);


# concatenate two or more sequences with annotations and features,
# the first sequence will be modified
FAST::Bio::SeqUtils->cat(@seqs);

# truncate a sequence, retaining features and adjusting their
# coordinates if necessary
my $truncseq = FAST::Bio::SeqUtils->trunc_with_features($seq, 100, 200);

# reverse complement a sequence and its features
my $revcomseq = FAST::Bio::SeqUtils->revcom_with_features($seq);

DESCRIPTION

This class is a holder of methods that work on FAST::Bio::PrimarySeqI- compliant sequence objects, e.g. FAST::Bio::PrimarySeq and FAST::Bio::Seq. These methods are not part of the FAST::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 FAST::Bio::PrimarySeqI, FAST::Bio::PrimarySeq, and FAST::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 FAST::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:

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

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   : $string = FAST::Bio::SeqUtils->seq3($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   : $seq = FAST::Bio::SeqUtils->seq3in($seq, 'MetGlyTer')
Function: Method for changing of the sequence of a
          FAST::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 : FAST::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 = FAST::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 FAST::Bio::PrimarySeqI::translate

translate_6frames

Title   : translate_6frames
Usage   : @prots = FAST::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 FAST::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   : FAST::Bio::SeqUtils->mutate($seq,$mutation1, $mutation2);
Function: Inplace editing of the sequence.

          The second argument can be a FAST::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 FAST::Bio::LiveSeq::Mutation object, or an array of them

See FAST::Bio::LiveSeq::Mutation.

cat

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

_coord_adjust

Title   : _coord_adjust
Usage   : my $newfeat=FAST::Bio::SeqUtils->_coord_adjust($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 FAST::Bio::Location::Fuzzy objects.

Returns : A FAST::Bio::SeqFeatureI compliant object.
Args    : A FAST::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   : $revcom=FAST::Bio::SeqUtils->revcom_with_features($seq);
Function: Like FAST::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 $newfeat=FAST::Bio::SeqUtils->_feature_revcom($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 FAST::Bio::SeqFeatureI compliant object.
Args    : A FAST::Bio::SeqFeatureI compliant object,
          the length of the parent sequence

evolve

Title   : evolve
Usage   : my $newseq = FAST::Bio::SeqUtils->
              evolve($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 FAST::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 FAST::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.