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 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://github.com/bioperl/bioperl-live/issuesAUTHOR - 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($seq)
Function: Translate a nucleotide sequence in three forward frames.
The IDs of the sequences are appended with '-0F', '-1F', '-2F'.
Returns : An array of seq objects
Args : sequence object
same arguments as to Bio::PrimarySeqI::translatetranslate_6frames
Title : translate_6frames
Usage : @prots = Bio::SeqUtils->translate_6frames($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 : 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 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)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 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.