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 listsSupport
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 : $string = Bio::SeqUtils->seq3($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($seq)
Function: Translate a nucleotide sequence in three forward frames.
The IDs of the sequences are appended with '-0F', '-1F', '-2F'.
Returns : An array of seq objects
Args : sequence object
same arguments as to Bio::PrimarySeqI::translatetranslate_6frames
Title : translate_6frames
Usage : @prots = Bio::SeqUtils->translate_6frames($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::translatevalid_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 themcat
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 objectsNote 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 sequencerevcom_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 sequenceevolve
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.