Bio::Variation VariantI
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Summary
Bio::Variation::VariantI - Sequence Change SeqFeature abstract class
Package variables
No package variables defined.
Inherit
Bio::DBLinkContainerI Bio::Root::Root Bio::SeqFeature::Generic
Synopsis
  #get Bio::Variant::VariantI somehow
print $var->restriction_changes, "\n";
foreach $allele ($var->each_Allele) {
#work on Bio::Variation::Allele objects
}
Description
This superclass defines common methods to basic sequence changes. The
instantiable classes Bio::Variation::DNAMutation,
Bio::Variation::RNAChange and Bio::Variation::AAChange use them.
See Bio::Variation::DNAMutation, Bio::Variation::RNAChange,
and Bio::Variation::AAChange for more information.
These classes store information, heavy computation to detemine allele
sequences is done elsewhere.
The database cross-references are implemented as
Bio::Annotation::DBLink objects. The methods to access them are
defined in Bio::DBLinkContainerI. See Bio::Annotation::DBLink
and Bio::DBLinkContainerI for details.
Bio::Variation::VariantI redifines and extends
Bio::SeqFeature::Generic for sequence variations. This class
describes specific sequence change events. These events are always
from a specific reference sequence to something different. See
Bio::SeqFeature::Generic for more information.
IMPORTANT: The notion of reference sequence permeates all
Bio::Variation classes. This is especially important to remember when
dealing with Alleles. In a polymorphic site, there can be a large
number of alleles. One of then has to be selected to be the reference
allele (allele_ori). ALL the rest has to be passed to the Variant
using the method add_Allele, including the mutated allele in a
canonical mutation. The IO modules and generated attributes depend on
it. They ignore the allele linked to using allele_mut and circulate
each Allele returned by each_Allele into allele_mut and calculate
the changes between that and allele_ori.
Methods
idDescriptionCode
add_AlleleDescriptionCode
each_AlleleDescriptionCode
isMutationDescriptionCode
allele_oriDescriptionCode
allele_mutDescriptionCode
lengthDescriptionCode
upStreamSeqDescriptionCode
dnStreamSeqDescriptionCode
labelDescriptionCode
statusDescriptionCode
proofDescriptionCode
regionDescriptionCode
region_valueDescriptionCode
region_distDescriptionCode
numberingDescriptionCode
mut_numberDescriptionCode
SeqDiffDescriptionCode
add_DBLinkDescriptionCode
each_DBLinkDescriptionCode
restriction_changesDescriptionCode
_revcompl
No description
Code
_enzymes
No description
Code
Methods description
idcode    nextTop
 Title   : id
Usage : $obj->id
Function:
Read only method. Returns the id of the variation object. The id is the id of the first DBLink object attached to this object. Example : Returns : scalar Args : none
add_AllelecodeprevnextTop
 Title   : add_Allele
Usage : $self->add_Allele($allele)
Function:
Adds one Bio::Variation::Allele into the list of alleles. Note that the method forces the convention that nucleotide sequence is in lower case and amino acds are in upper case. Example : Returns : 1 when succeeds, 0 for failure. Args : Allele object
each_AllelecodeprevnextTop
 Title   : alleles
Usage : $obj->each_Allele();
Function:
Returns a list of Bio::Variation::Allele objects Example : Returns : list of Alleles Args : none
isMutationcodeprevnextTop
 Title   : isMutation
Usage : print join('/', $obj->each_Allele) if not $obj->isMutation;
Function:
Returns or sets the boolean value indicating that the variant descibed is a canonical mutation with two alleles assinged to be the original (wild type) allele and mutated allele, respectively. If this value is not set, it is assumed that the Variant descibes polymorphisms. Returns : a boolean
allele_oricodeprevnextTop
 Title   : allele_ori
Usage : $obj->allele_ori();
Function:
Links to and returns the Bio::Variation::Allele object. If value is not set, returns false. All other Alleles are compared to this. Amino acid sequences are stored in upper case characters, others in lower case. Example : Returns : string Args : string
See Bio::Variation::Allele for more.
allele_mutcodeprevnextTop
 Title   : allele_mut
Usage : $obj->allele_mut();
Function:
Links to and returns the Bio::Variation::Allele object. Sets and returns the mutated allele sequence. If value is not set, returns false. Amino acid sequences are stored in upper case characters, others in lower case. Example : Returns : string Args : string
See Bio::Variation::Allele for more.
lengthcodeprevnextTop
 Title   : length
Usage : $obj->length();
Function:
Sets and returns the length of the affected original allele sequence. If value is not set, returns false == 0. Value 0 means that the variant position is before the start=end sequence position. (Value 1 would denote a point mutation). This follows the convension to report an insertion (2insT) in equivalent way to a corresponding deletion (2delT) (Think about indel polymorpism ATC <=> AC where the origianal state is not known ). Example : Returns : string Args : string
upStreamSeqcodeprevnextTop
 Title   : upStreamSeq
Usage : $obj->upStreamSeq();
Function:
Sets and returns upstream flanking sequence string. If value is not set, returns false. The sequence should be >=25 characters long, if possible. Example : Returns : string or false Args : string
dnStreamSeqcodeprevnextTop
 Title   : dnStreamSeq
Usage : $obj->dnStreamSeq();
Function:
Sets and returns dnstream flanking sequence string. If value is not set, returns false. The sequence should be >=25 characters long, if possible. Example : Returns : string or false Args : string
labelcodeprevnextTop
 Title   : label
Usage : $obj->label();
Function:
Sets and returns mutation event label(s). If value is not set, or no argument is given returns false. Each instantiable class needs to implement this method. Valid values are listed in 'Mutation event controlled vocabulary' in http://www.ebi.ac.uk/mutations/recommendations/mutevent.html.
Example : Returns : string Args : string
statuscodeprevnextTop
 Title   : status
Usage : $obj->status()
Function:
Returns the status of the sequence change object. Valid values are: 'suspected' and 'proven' Example : $obj->status('proven'); Returns : scalar Args : valid string (optional, for setting)
proofcodeprevnextTop
 Title   : proof
Usage : $obj->proof()
Function:
Returns the proof of the sequence change object. Valid values are: 'computed' and 'experimental'. Example : $obj->proof('computed'); Returns : scalar Args : valid string (optional, for setting)
regioncodeprevnextTop
 Title   : region
Usage : $obj->region();
Function:
Sets and returns the name of the sequence region type or protein domain at this location. If value is not set, returns false. Example : Returns : string Args : string
region_valuecodeprevnextTop
 Title   : region_value
Usage : $obj->region_value();
Function:
Sets and returns the name of the sequence region_value or protein domain at this location. If value is not set, returns false. Example : Returns : string Args : string
region_distcodeprevnextTop
 Title   : region_dist
Usage : $obj->region_dist();
Function:
Sets and returns the distance tot the closest region (i.e. intro/exon or domain) boundary. If distance is not set, returns false. Example : Returns : integer Args : integer
numberingcodeprevnextTop
 Title   : numbering
Usage : $obj->numbering()
Function:
Returns the numbering chema used locating sequnce features. Valid values are: 'entry' and 'coding' Example : $obj->numbering('coding'); Returns : scalar Args : valid string (optional, for setting)
mut_numbercodeprevnextTop
 Title   : mut_number
Usage : $num = $obj->mut_number;
: $num = $obj->mut_number($number);
Function:
Returns or sets the number identifying the order in which the mutation has been issued. Numbers shouldstart from 1. If the number has never been set, the method will return '' If you want the output from IO modules look nice and, for multivariant/allele variations, make sense you better set this attribute. Returns : an integer
SeqDiffcodeprevnextTop
 Title   : SeqDiff
Usage : $mutobj = $obj->SeqDiff;
: $mutobj = $obj->SeqDiff($objref);
Function:
Returns or sets the link-reference to the umbrella Bio::Variation::SeqDiff object. If there is no link, it will return undef Note: Adding a variant into a SeqDiff object will automatically set this value. Returns : an obj_ref or undef
See Bio::Variation::SeqDiff for more information.
add_DBLinkcodeprevnextTop
 Title   : add_DBLink
Usage : $self->add_DBLink($ref)
Function: adds a link object
Example :
Returns :
Args :
each_DBLinkcodeprevnextTop
 Title   : each_DBLink
Usage : foreach $ref ( $self->each_DBlink() )
Function: gets an array of DBlink of objects
Example :
Returns :
Args :
restriction_changescodeprevnextTop
 Title   : restriction_changes
Usage : $obj->restriction_changes();
Function:
Returns a string containing a list of restriction enzyme changes of form +EcoRI, separated by commas. Strings need to be valid restriction enzyme names as stored in REBASE. allele_ori and allele_mut need to be assigned. Example : Returns : string Args : string
Methods code
iddescriptionprevnextTop
sub id {
   my ($self) = @_;
   my @ids = $self->each_DBLink;
   my $id = $ids[0] if scalar @ids > 0;
   return $id->database. "::". $id->primary_id if $id;
}
add_AlleledescriptionprevnextTop
sub add_Allele {
  my ($self,$value) = @_;
  if (defined $value) {
      if( ! $value->isa('Bio::Variation::Allele') ) {
	  my $com = ref $value;
	  $self->throw("Is not a Allele object but a  [$com]");
	  return 0;
      } else {
	  if ( $self->isa('Bio::Variation::AAChange') ) {
	      $value->seq( uc $value->seq) if $value->seq;
	  } else {
	      $value->seq( lc $value->seq) if $value->seq;
	  } 
	  push(@{$self->{'alleles'}},$value); 
	  $self->allele_mut($value); #????
return 1; } } else { return 0; }
}
each_AlleledescriptionprevnextTop
sub each_Allele {
   my ($self,@args) = @_;
   return @{$self->{'alleles'}};
}
isMutationdescriptionprevnextTop
sub isMutation {
    my ($self,$value) = @_;
    if (defined $value) {
        if ($value ) {
            $self->{'isMutation'} = 1;
        } else {
            $self->{'isMutation'} = 0;
        }
    }
    return $self->{'isMutation'};
}
allele_oridescriptionprevnextTop
sub allele_ori {
   my ($self,$value) = @_;
   if( defined $value) {
       if ( ! ref $value || ! $value->isa('Bio::Variation::Allele')) {
	   $self->throw("Value is not Bio::Variation::Allele but [$value]");
       } else {
	   if ( $self->isa('Bio::Variation::AAChange') ) {
	       $value->seq( uc $value->seq) if $value->seq;
	   } else {
	       $value->seq( lc $value->seq) if $value->seq;
	   } 
	   $self->{'allele_ori'} = $value;
       }
   }
   return $self->{'allele_ori'};
}
allele_mutdescriptionprevnextTop
sub allele_mut {
   my ($self,$value) = @_;
   if( defined $value) {
       if ( ! ref $value || ! $value->isa('Bio::Variation::Allele')) {
	   $self->throw("Value is not Bio::Variation::Allele but [$value]");
       } else {
	   if ( $self->isa('Bio::Variation::AAChange') ) {
	       $value->seq( uc $value->seq) if $value->seq;
	   } else {
	       $value->seq( lc $value->seq) if $value->seq;
	   } 
	   $self->{'allele_mut'} = $value;
       }
   }
   return $self->{'allele_mut'};
}
lengthdescriptionprevnextTop
sub length {
   my ($self,$value) = @_;
   if ( defined $value) {
       $self->{'length'} = $value;
  }
   if ( ! exists $self->{'length'} ) {
       return 0;
   } 
   return $self->{'length'};
}
upStreamSeqdescriptionprevnextTop
sub upStreamSeq {
    my ($self,$value) = @_;
    if( defined $value) {
	$self->{'upstreamseq'} = $value;
    }
   return $self->{'upstreamseq'};
}
dnStreamSeqdescriptionprevnextTop
sub dnStreamSeq {
    my ($self,$value) = @_;
    if( defined $value) {
	$self->{'dnstreamseq'} = $value;
    }
    return $self->{'dnstreamseq'};
}
labeldescriptionprevnextTop
sub label {
    my ($self,$value) = @_;
    $self->throw_not_implemented();
}
statusdescriptionprevnextTop
sub status {
   my ($self,$value) = @_;
   my %status = (suspected => 1,
		 proven => 1
		 );

   if( defined $value) {
       $value = lc $value;
       if ($status{$value}) {
	   $self->{'status'} = $value;
       } 
       else {
	   $self->throw("$value is not valid status value!");
       }
    }
   if( ! exists $self->{'status'} ) {
       return "$self";
   }
   return $self->{'status'};
}
proofdescriptionprevnextTop
sub proof {
    my ($self,$value) = @_;
    my %proof = (computed => 1,
		 experimental => 1
		 );

    if( defined $value) {
	$value = lc $value;
	if ($proof{$value}) {
	    $self->{'proof'} = $value;
	} else {
	    $self->throw("$value is not valid proof value!");
	}
    }
    return $self->{'proof'};
}
regiondescriptionprevnextTop
sub region {
    my ($self,$value) = @_;
    if( defined $value) {
	$self->{'region'} = $value;
    }
    return $self->{'region'};
}
region_valuedescriptionprevnextTop
sub region_value {
    my ($self,$value) = @_;
    if( defined $value) {
	$self->{'region_value'} = $value;
    }
    return $self->{'region_value'};
}
region_distdescriptionprevnextTop
sub region_dist {
    my ($self,$value) = @_;
    if( defined $value) {
       if (  not $value =~ /^[+-]?\d+$/ ) {
	   $self->throw("[$value] for region_dist has to be an integer\n");
        } else {
	    $self->{'region_dist'} = $value;
        }
    }
    return $self->{'region_dist'};
}
numberingdescriptionprevnextTop
sub numbering {
   my ($self,$value) = @_;
   my %numbering = (entry => 1,
		    coding => 1
		    );

   if( defined $value) {
       $value = lc $value;
       if ($numbering{$value}) {
	   $self->{'numbering'} = $value;
       } 
       else {
	   $self->throw("'$value' is not a valid for numbering!");
       }
    }
   if( ! exists $self->{'numbering'} ) {
       return "$self";
   }
   return $self->{'numbering'};
}
mut_numberdescriptionprevnextTop
sub mut_number {
    my ($self,$value) = @_;
    if (defined $value) {
	$self->{'mut_number'} = $value;
    }
    unless (exists $self->{'mut_number'}) {
	return ('');
    } else {
	return $self->{'mut_number'};
    }
}
SeqDiffdescriptionprevnextTop
sub SeqDiff {
    my ($self,$value) = @_;
    if (defined $value) {
	if( ! $value->isa('Bio::Variation::SeqDiff') ) {
	    $self->throw("Is not a Bio::Variation::SeqDiff object but a [$value]");
	    return;
	}
	else {
	    $self->{'seqDiff'} = $value;
	}
    }
    unless (exists $self->{'seqDiff'}) {
	return;
    } else {
	return $self->{'seqDiff'};
    }
}
add_DBLinkdescriptionprevnextTop
sub add_DBLink {
   my ($self,$com) = @_;
   if( $com && ! $com->isa('Bio::Annotation::DBLink') ) {
       $self->throw("Is not a link object but a  [$com]");
   }
   $com && push(@{$self->{'link'}},$com);
}
each_DBLinkdescriptionprevnextTop
sub each_DBLink {
   my ($self) = @_;
   
   return @{$self->{'link'}};
}
restriction_changesdescriptionprevnextTop
sub restriction_changes {
     my ($self) = @_;

    if (not $self->{'re_changes'}) { 
	my %re = &_enzymes;
	
	# complain if used on AA data
if ($self->isa('Bio::Variation::AAChange')) { $self->throw('Restriction enzymes do not bite polypeptides!'); } #sanity checks
$self->warn('Upstream sequence is empty!') if $self->upStreamSeq eq ''; $self->warn('Downstream sequence is empty!') if $self->dnStreamSeq eq ''; # $self->warn('Original allele sequence is empty!')
# if $self->allele_ori eq '';
# $self->warn('Mutated allele sequence is empty!')
# if $self->allele_mut eq '';
#reuse the non empty DNA level list at RNA level if the flanks are identical
#Hint: Check DNAMutation object first
if ($self->isa('Bio::Variation::RNAChange') and $self->DNAMutation and $self->upStreamSeq eq $self->DNAMutation->upStreamSeq and $self->dnStreamSeq eq $self->DNAMutation->dnStreamSeq and $self->DNAMutation->restriction_changes ne '' ) { $self->{'re_changes'} = $self->DNAMutation->restriction_changes; } else { #maximum length of a type II restriction site in the current REBASE
my ($le_dn) = 15; my ($le_up) = $le_dn; #reduce the flank lengths if the desired length is not available
$le_dn = CORE::length ($self->dnStreamSeq) if $le_dn > CORE::length ($self->dnStreamSeq); $le_up = CORE::length ($self->upStreamSeq) if $le_up > CORE::length ($self->upStreamSeq); #Build sequence strings to compare
my ($oriseq, $mutseq); $oriseq = $mutseq = substr($self->upStreamSeq, -$le_up, $le_up); $oriseq .= $self->allele_ori->seq if $self->allele_ori->seq; $mutseq .= $self->allele_mut->seq if $self->allele_mut->seq; $oriseq .= substr($self->dnStreamSeq, 0, $le_dn); $mutseq .= substr($self->dnStreamSeq, 0, $le_dn); # ... and their reverse complements
my $oriseq_rev = _revcompl ($oriseq); my $mutseq_rev = _revcompl ($mutseq); # collect results into a string
my $rec = ''; foreach my $enz (sort keys (%re)) { my $site = $re{$enz}; my @ori = ($oriseq=~ /$site/g); my @mut = ($mutseq=~ /$site/g); my @ori_r = ($oriseq_rev =~ /$site/g); my @mut_r = ($mutseq_rev =~ /$site/g); $rec .= '+'. $enz. ", " if (scalar @ori < scalar @mut) or (scalar @ori_r < scalar @mut_r); $rec .= '-'. $enz. ", " if (scalar @ori > scalar @mut) or (scalar @ori_r > scalar @mut_r); } $rec = substr($rec, 0, CORE::length($rec) - 2) if $rec ne ''; $self->{'re_changes'} = $rec; } } return $self->{'re_changes'}
}
_revcompldescriptionprevnextTop
sub _revcompl {
     # side effect: lower case letters
my ($seq) = shift; $seq = lc $seq; $seq =~ tr/acgtrymkswhbvdnx/tgcayrkmswdvbhnx/; return CORE::reverse $seq;
}
_enzymesdescriptionprevnextTop
sub _enzymes {
 #REBASE version 005   type2.005
my %enzymes = ( 'AarI' => 'cacctgc', 'AatII' => 'gacgtc', 'AccI' => 'gt[ac][gt]ac', 'AceIII' => 'cagctc', 'AciI' => 'ccgc', 'AclI' => 'aacgtt', 'AcyI' => 'g[ag]cg[ct]c', 'AflII' => 'cttaag', 'AflIII' => 'ac[ag][ct]gt', 'AgeI' => 'accggt', 'AhaIII' => 'tttaaa', 'AloI' => 'gaac[acgt][acgt][acgt][acgt][acgt][acgt]tcc', 'AluI' => 'agct', 'AlwNI' => 'cag[acgt][acgt][acgt]ctg', 'ApaBI' => 'gca[acgt][acgt][acgt][acgt][acgt]tgc', 'ApaI' => 'gggccc', 'ApaLI' => 'gtgcac', 'ApoI' => '[ag]aatt[ct]', 'AscI' => 'ggcgcgcc', 'AsuI' => 'gg[acgt]cc', 'AsuII' => 'ttcgaa', 'AvaI' => 'c[ct]cg[ag]g', 'AvaII' => 'gg[at]cc', 'AvaIII' => 'atgcat', 'AvrII' => 'cctagg', 'BaeI' => 'ac[acgt][acgt][acgt][acgt]gta[ct]c', 'BalI' => 'tggcca', 'BamHI' => 'ggatcc', 'BbvCI' => 'cctcagc', 'BbvI' => 'gcagc', 'BbvII' => 'gaagac', 'BccI' => 'ccatc', 'Bce83I' => 'cttgag', 'BcefI' => 'acggc', 'BcgI' => 'cga[acgt][acgt][acgt][acgt][acgt][acgt]tgc', 'BciVI' => 'gtatcc', 'BclI' => 'tgatca', 'BetI' => '[at]ccgg[at]', 'BfiI' => 'actggg', 'BglI' => 'gcc[acgt][acgt][acgt][acgt][acgt]ggc', 'BglII' => 'agatct', 'BinI' => 'ggatc', 'BmgI' => 'g[gt]gccc', 'BplI' => 'gag[acgt][acgt][acgt][acgt][acgt]ctc', 'Bpu10I' => 'cct[acgt]agc', 'BsaAI' => '[ct]acgt[ag]', 'BsaBI' => 'gat[acgt][acgt][acgt][acgt]atc', 'BsaXI' => 'ac[acgt][acgt][acgt][acgt][acgt]ctcc', 'BsbI' => 'caacac', 'BscGI' => 'cccgt', 'BseMII' => 'ctcag', 'BsePI' => 'gcgcgc', 'BseRI' => 'gaggag', 'BseSI' => 'g[gt]gc[ac]c', 'BsgI' => 'gtgcag', 'BsiI' => 'cacgag', 'BsiYI' => 'cc[acgt][acgt][acgt][acgt][acgt][acgt][acgt]gg', 'BsmAI' => 'gtctc', 'BsmI' => 'gaatgc', 'Bsp1407I' => 'tgtaca', 'Bsp24I' => 'gac[acgt][acgt][acgt][acgt][acgt][acgt]tgg', 'BspGI' => 'ctggac', 'BspHI' => 'tcatga', 'BspLU11I' => 'acatgt', 'BspMI' => 'acctgc', 'BspMII' => 'tccgga', 'BsrBI' => 'ccgctc', 'BsrDI' => 'gcaatg', 'BsrI' => 'actgg', 'BstEII' => 'ggt[acgt]acc', 'BstXI' => 'cca[acgt][acgt][acgt][acgt][acgt][acgt]tgg', 'BtrI' => 'cacgtc', 'BtsI' => 'gcagtg', 'Cac8I' => 'gc[acgt][acgt]gc', 'CauII' => 'cc[cg]gg', 'Cfr10I' => '[ag]ccgg[ct]', 'CfrI' => '[ct]ggcc[ag]', 'CjeI' => 'cca[acgt][acgt][acgt][acgt][acgt][acgt]gt', 'CjePI' => 'cca[acgt][acgt][acgt][acgt][acgt][acgt][acgt]tc', 'ClaI' => 'atcgat', 'CviJI' => '[ag]gc[ct]', 'CviRI' => 'tgca', 'DdeI' => 'ct[acgt]ag', 'DpnI' => 'gatc', 'DraII' => '[ag]gg[acgt]cc[ct]', 'DraIII' => 'cac[acgt][acgt][acgt]gtg', 'DrdI' => 'gac[acgt][acgt][acgt][acgt][acgt][acgt]gtc', 'DrdII' => 'gaacca', 'DsaI' => 'cc[ag][ct]gg', 'Eam1105I' => 'gac[acgt][acgt][acgt][acgt][acgt]gtc', 'EciI' => 'ggcgga', 'Eco31I' => 'ggtctc', 'Eco47III' => 'agcgct', 'Eco57I' => 'ctgaag', 'EcoNI' => 'cct[acgt][acgt][acgt][acgt][acgt]agg', 'EcoRI' => 'gaattc', 'EcoRII' => 'cc[at]gg', 'EcoRV' => 'gatatc', 'Esp3I' => 'cgtctc', 'EspI' => 'gct[acgt]agc', 'FauI' => 'cccgc', 'FinI' => 'gggac', 'Fnu4HI' => 'gc[acgt]gc', 'FnuDII' => 'cgcg', 'FokI' => 'ggatg', 'FseI' => 'ggccggcc', 'GdiII' => 'cggcc[ag]', 'GsuI' => 'ctggag', 'HaeI' => '[at]ggcc[at]', 'HaeII' => '[ag]gcgc[ct]', 'HaeIII' => 'ggcc', 'HaeIV' => 'ga[ct][acgt][acgt][acgt][acgt][acgt][ag]tc', 'HgaI' => 'gacgc', 'HgiAI' => 'g[at]gc[at]c', 'HgiCI' => 'gg[ct][ag]cc', 'HgiEII' => 'acc[acgt][acgt][acgt][acgt][acgt][acgt]ggt', 'HgiJII' => 'g[ag]gc[ct]c', 'HhaI' => 'gcgc', 'Hin4I' => 'ga[cgt][acgt][acgt][acgt][acgt][acgt][acg]tc', 'HindII' => 'gt[ct][ag]ac', 'HindIII' => 'aagctt', 'HinfI' => 'ga[acgt]tc', 'HpaI' => 'gttaac', 'HpaII' => 'ccgg', 'HphI' => 'ggtga', 'Hpy178III' => 'tc[acgt][acgt]ga', 'Hpy188I' => 'tc[acgt]ga', 'Hpy99I' => 'cg[at]cg', 'KpnI' => 'ggtacc', 'Ksp632I' => 'ctcttc', 'MaeI' => 'ctag', 'MaeII' => 'acgt', 'MaeIII' => 'gt[acgt]ac', 'MboI' => 'gatc', 'MboII' => 'gaaga', 'McrI' => 'cg[ag][ct]cg', 'MfeI' => 'caattg', 'MjaIV' => 'gt[acgt][acgt]ac', 'MluI' => 'acgcgt', 'MmeI' => 'tcc[ag]ac', 'MnlI' => 'cctc', 'MseI' => 'ttaa', 'MslI' => 'ca[ct][acgt][acgt][acgt][acgt][ag]tg', 'MstI' => 'tgcgca', 'MwoI' => 'gc[acgt][acgt][acgt][acgt][acgt][acgt][acgt]gc', 'NaeI' => 'gccggc', 'NarI' => 'ggcgcc', 'NcoI' => 'ccatgg', 'NdeI' => 'catatg', 'NheI' => 'gctagc', 'NlaIII' => 'catg', 'NlaIV' => 'gg[acgt][acgt]cc', 'NotI' => 'gcggccgc', 'NruI' => 'tcgcga', 'NspBII' => 'c[ac]gc[gt]g', 'NspI' => '[ag]catg[ct]', 'PacI' => 'ttaattaa', 'Pfl1108I' => 'tcgtag', 'PflMI' => 'cca[acgt][acgt][acgt][acgt][acgt]tgg', 'PleI' => 'gagtc', 'PmaCI' => 'cacgtg', 'PmeI' => 'gtttaaac', 'PpiI' => 'gaac[acgt][acgt][acgt][acgt][acgt]ctc', 'PpuMI' => '[ag]gg[at]cc[ct]', 'PshAI' => 'gac[acgt][acgt][acgt][acgt]gtc', 'PsiI' => 'ttataa', 'PstI' => 'ctgcag', 'PvuI' => 'cgatcg', 'PvuII' => 'cagctg', 'RleAI' => 'cccaca', 'RsaI' => 'gtac', 'RsrII' => 'cgg[at]ccg', 'SacI' => 'gagctc', 'SacII' => 'ccgcgg', 'SalI' => 'gtcgac', 'SanDI' => 'ggg[at]ccc', 'SapI' => 'gctcttc', 'SauI' => 'cct[acgt]agg', 'ScaI' => 'agtact', 'ScrFI' => 'cc[acgt]gg', 'SduI' => 'g[agt]gc[act]c', 'SecI' => 'cc[acgt][acgt]gg', 'SexAI' => 'acc[at]ggt', 'SfaNI' => 'gcatc', 'SfeI' => 'ct[ag][ct]ag', 'SfiI' => 'ggcc[acgt][acgt][acgt][acgt][acgt]ggcc', 'SgfI' => 'gcgatcgc', 'SgrAI' => 'c[ag]ccgg[ct]g', 'SimI' => 'gggtc', 'SmaI' => 'cccggg', 'SmlI' => 'ct[ct][ag]ag', 'SnaBI' => 'tacgta', 'SnaI' => 'gtatac', 'SpeI' => 'actagt', 'SphI' => 'gcatgc', 'SplI' => 'cgtacg', 'SrfI' => 'gcccgggc', 'Sse232I' => 'cgccggcg', 'Sse8387I' => 'cctgcagg', 'Sse8647I' => 'agg[at]cct', 'SspI' => 'aatatt', 'Sth132I' => 'cccg', 'StuI' => 'aggcct', 'StyI' => 'cc[at][at]gg', 'SwaI' => 'atttaaat', 'TaqI' => 'tcga', 'TaqII' => 'gaccga', 'TatI' => '[at]gtac[at]', 'TauI' => 'gc[cg]gc', 'TfiI' => 'ga[at]tc', 'TseI' => 'gc[at]gc', 'Tsp45I' => 'gt[cg]ac', 'Tsp4CI' => 'ac[acgt]gt', 'TspEI' => 'aatt', 'TspRI' => 'ca[cg]tg[acgt][acgt]', 'Tth111I' => 'gac[acgt][acgt][acgt]gtc', 'Tth111II' => 'caa[ag]ca', 'UbaGI' => 'cac[acgt][acgt][acgt][acgt]gtg', 'UbaPI' => 'cgaacg', 'VspI' => 'attaat', 'XbaI' => 'tctaga', 'XcmI' => 'cca[acgt][acgt][acgt][acgt][acgt][acgt][acgt][acgt][acgt]tgg', 'XhoI' => 'ctcgag', 'XhoII' => '[ag]gatc[ct]', 'XmaIII' => 'cggccg', 'XmnI' => 'gaa[acgt][acgt][acgt][acgt]ttc' ); return %enzymes; } 1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to 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 Top
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 BugsTop
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 LehvaslaihoTop
Email: heikki-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _