Bio::Tools CodonTable
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Tools::CodonTable - Bioperl codon table object
Package variables
No package variables defined.
Included modules
Bio::SeqUtils
Bio::Tools::IUPAC
Inherit
Bio::Root::Root
Synopsis
  # This is a read-only class for all known codon tables.  The IDs are
# the ones used by nucleotide sequence databases. All common IUPAC
# ambiguity codes for DNA, RNA and animo acids are recognized.
# to use use Bio::Tools::CodonTable; # defaults to ID 1 "Standard" $myCodonTable = Bio::Tools::CodonTable->new(); $myCodonTable2 = Bio::Tools::CodonTable->new( -id => 3 ); # change codon table $myCodonTable->id(5); # examine codon table print join (' ', "The name of the codon table no.", $myCodonTable->id(4), "is:", $myCodonTable->name(), "\n"); # print possible codon tables $tables = Bio::Tools::CodonTable->tables; while ( ($id,$name) = each %{$tables} ) { print "$id = $name\n"; } # translate a codon $aa = $myCodonTable->translate('ACU'); $aa = $myCodonTable->translate('act'); $aa = $myCodonTable->translate('ytr'); # reverse translate an amino acid @codons = $myCodonTable->revtranslate('A'); @codons = $myCodonTable->revtranslate('Ser'); @codons = $myCodonTable->revtranslate('Glx'); @codons = $myCodonTable->revtranslate('cYS', 'rna'); # reverse translate an entire amino acid sequence into a IUPAC # nucleotide string my $seqobj = Bio::PrimarySeq->new(-seq => 'FHGERHEL'); my $iupac_str = $myCodonTable->reverse_translate_all($seqobj); #boolean tests print "Is a start\n" if $myCodonTable->is_start_codon('ATG'); print "Is a termianator\n" if $myCodonTable->is_ter_codon('tar'); print "Is a unknown\n" if $myCodonTable->is_unknown_codon('JTG');
Description
Codon tables are also called translation tables or genetic codes
since that is what they represent. A bit more complete picture
of the full complexity of codon usage in various taxonomic groups
is presented at the NCBI Genetic Codes Home page.
CodonTable is a BioPerl class that knows all current translation
tables that are used by primary nucleotide sequence databases
(GenBank, EMBL and DDBJ). It provides methods to output information
about tables and relationships between codons and amino acids.
This class and its methods recognized all common IUPAC ambiguity codes
for DNA, RNA and animo acids. The translation method follows the
conventions in EMBL and TREMBL databases.
It is a nuisance to separate RNA and cDNA representations of nucleic
acid transcripts. The CodonTable object accepts codons of both type as
input and allows the user to set the mode for output when reverse
translating. Its default for output is DNA.
Note:
This class deals primarily with individual codons and amino
acids. However in the interest of speed you can translate
longer sequence, too. The full complexity of protein translation
is tackled by Bio::PrimarySeqI::translate.
The amino acid codes are IUPAC recommendations for common amino acids:
          A           Ala            Alanine
R Arg Arginine
N Asn Asparagine
D Asp Aspartic acid
C Cys Cysteine
Q Gln Glutamine
E Glu Glutamic acid
G Gly Glycine
H His Histidine
I Ile Isoleucine
L Leu Leucine
K Lys Lysine
M Met Methionine
F Phe Phenylalanine
P Pro Proline
O Pyl Pyrrolysine (22nd amino acid)
U Sec Selenocysteine (21st amino acid)
S Ser Serine
T Thr Threonine
W Trp Tryptophan
Y Tyr Tyrosine
V Val Valine
B Asx Aspartic acid or Asparagine
Z Glx Glutamine or Glutamic acid
J Xle Isoleucine or Valine (mass spec ambiguity)
X Xaa Any or unknown amino acid
It is worth noting that, "Bacterial" codon table no. 11 produces an
polypeptide that is, confusingly, identical to the standard one. The
only differences are in available initiator codons.
NCBI Genetic Codes home page:
http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c
EBI Translation Table Viewer:
http://www.ebi.ac.uk/cgi-bin/mutations/trtables.cgi
Amended ASN.1 version with ids 16 and 21 is at:
ftp://ftp.ebi.ac.uk/pub/databases/geneticcode/
Thanks to Matteo diTomasso for the original Perl implementation
of these tables.
Methods
BEGIN Code
new
No description
Code
idDescriptionCode
nameDescriptionCode
tablesDescriptionCode
translateDescriptionCode
_translate_ambiguous_codon
No description
Code
translate_strictDescriptionCode
revtranslateDescriptionCode
reverse_translate_allDescriptionCode
is_start_codonDescriptionCode
is_ter_codonDescriptionCode
is_unknown_codonDescriptionCode
_unambiquous_codonsDescriptionCode
add_tableDescriptionCode
_make_iupac_string
No description
Code
Methods description
idcode    nextTop
 Title   : id
Usage : $obj->id(3); $id_integer = $obj->id();
Function:
Sets or returns the id of the translation table. IDs are integers from 1 to 15, excluding 7 and 8 which have been removed as redundant. If an invalid ID is given the method returns 0, false. Example : Returns : value of id, a scalar, 0 if not a valid Args : newvalue (optional)
namecodeprevnextTop
 Title   : name
Usage : $obj->name()
Function: returns the descriptive name of the translation table
Example :
Returns : A string
Args : None
tablescodeprevnextTop
 Title   : tables
Usage : $obj->tables() or Bio::Tools::CodonTable->tables()
Function: returns a hash reference where each key is a valid codon
table id() number, and each value is the corresponding
codon table name() string
Example :
Returns : A hashref
Args : None
translatecodeprevnextTop
 Title   : translate
Usage : $obj->translate('YTR')
Function: Returns a string of one letter amino acid codes from
nucleotide sequence input. The imput can be of any length.
Returns 'X' for unknown codons and codons that code for more than one amino acid. Returns an empty string if input is not three characters long. Exceptions for these are: - IUPAC amino acid code B for Aspartic Acid and Asparagine, is used. - IUPAC amino acid code Z for Glutamic Acid, Glutamine is used. - if the codon is two nucleotides long and if by adding an a third character 'N', it codes for a single amino acid (with exceptions above), return that, otherwise return empty string. Returns empty string for other input strings that are not three characters long. Example : Returns : a string of one letter ambiguous IUPAC amino acid codes Args : ambiguous IUPAC nucleotide string
translate_strictcodeprevnextTop
 Title   : translate_strict
Usage : $obj->translate_strict('ACT')
Function: returns one letter amino acid code for a codon input
Fast and simple translation. User is responsible to resolve ambiguous nucleotide codes before calling this method. Returns 'X' for unknown codons and an empty string for input strings that are not three characters long. It is not recommended to use this method in a production environment. Use method translate, instead. Example : Returns : A string Args : a codon = a three nucleotide character string
revtranslatecodeprevnextTop
 Title   : revtranslate
Usage : $obj->revtranslate('G')
Function: returns codons for an amino acid
Returns an empty string for unknown amino acid codes. Ambiquous IUPAC codes Asx,B, (Asp,D; Asn,N) and Glx,Z (Glu,E; Gln,Q) are resolved. Both single and three letter amino acid codes are accepted. '*' and 'Ter' are used for terminator. By default, the output codons are shown in DNA. If the output is needed in RNA (tr/t/u/), add a second argument 'RNA'. Example : $obj->revtranslate('Gly', 'RNA') Returns : An array of three lower case letter strings i.e. codons Args : amino acid, 'RNA'
reverse_translate_allcodeprevnextTop
 Title   : reverse_translate_all
Usage : my $iup_str = $cttable->reverse_translate_all($seq_object)
my $iup_str = $cttable->reverse_translate_all($seq_object,
$cutable,
15);
Function: reverse translates a protein sequence into IUPAC nucleotide
sequence. An 'X' in the protein sequence is converted to 'NNN'
in the nucleotide sequence.
Returns : a string
Args : a Bio::PrimarySeqI compatible object (mandatory)
a Bio::CodonUsage::Table object and a threshold if only
codons with a relative frequency above the threshold are
to be considered.
is_start_codoncodeprevnextTop
 Title   : is_start_codon
Usage : $obj->is_start_codon('ATG')
Function: returns true (1) for all codons that can be used as a
translation start, false (0) for others.
Example : $myCodonTable->is_start_codon('ATG')
Returns : boolean
Args : codon
is_ter_codoncodeprevnextTop
 Title   : is_ter_codon
Usage : $obj->is_ter_codon('GAA')
Function: returns true (1) for all codons that can be used as a
translation tarminator, false (0) for others.
Example : $myCodonTable->is_ter_codon('ATG')
Returns : boolean
Args : codon
is_unknown_codoncodeprevnextTop
 Title   : is_unknown_codon
Usage : $obj->is_unknown_codon('GAJ')
Function: returns false (0) for all codons that are valid,
true (1) for others.
Example : $myCodonTable->is_unknown_codon('NTG')
Returns : boolean
Args : codon
_unambiquous_codonscodeprevnextTop
 Title   : _unambiquous_codons
Usage : @codons = _unambiquous_codons('ACN')
Function:
Example :
Returns : array of strings (one letter unambiguous amino acid codes)
Args : a codon = a three IUPAC nucleotide character string
add_tablecodeprevnextTop
 Title   : add_table
Usage : $newid = $ct->add_table($name, $table, $starts)
Function: Add a custom Codon Table into the object.
Know what you are doing, only the length of
the argument strings is checked!
Returns : the id of the new codon table
Args : name, a string, optional (can be empty)
table, a string of 64 characters
startcodons, a string of 64 characters, defaults to standard
Methods code
BEGINTop
BEGIN {
     use constant CODONSIZE => 3;
    $GAP = '-';
    $CODONGAP = $GAP x CODONSIZE;

    @NAMES =			#id
( 'Standard', #1
'Vertebrate Mitochondrial',#2
'Yeast Mitochondrial',# 3
'Mold, Protozoan, and CoelenterateMitochondrial and Mycoplasma/Spiroplasma',#4
'Invertebrate Mitochondrial',#5
'Ciliate, Dasycladacean and Hexamita Nuclear',# 6
'', '', 'Echinoderm Mitochondrial',#9
'Euplotid Nuclear',#10
'"Bacterial"',# 11
'Alternative Yeast Nuclear',# 12
'Ascidian Mitochondrial',# 13
'Flatworm Mitochondrial',# 14
'Blepharisma Nuclear',# 15
'Chlorophycean Mitochondrial',# 16
'', '', '', '', 'Trematode Mitochondrial',# 21
'Scenedesmus obliquus Mitochondrial', #22
'Thraustochytrium Mitochondrial' #23
); @TABLES = qw( FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG '' '' FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG '' '' '' '' FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG ); @STARTS = qw( ---M---------------M---------------M---------------------------- --------------------------------MMMM---------------M------------ ----------------------------------MM---------------------------- --MM---------------M------------MMMM---------------M------------ ---M----------------------------MMMM---------------M------------ -----------------------------------M---------------------------- '' '' -----------------------------------M---------------------------- -----------------------------------M---------------------------- ---M---------------M------------MMMM---------------M------------ -------------------M---------------M---------------------------- -----------------------------------M---------------------------- -----------------------------------M---------------------------- -----------------------------------M---------------------------- -----------------------------------M---------------------------- '' '' '' '' -----------------------------------M---------------M------------ -----------------------------------M---------------------------- --------------------------------M--M---------------M------------ ); my @nucs = qw(t c a g); my $x = 0; ($CODONS, $TRCOL) = ({}, {}); for my $i (@nucs) { for my $j (@nucs) { for my $k (@nucs) { my $codon = "$i$j$k"; $CODONS->{$codon} = $x; $TRCOL->{$x} = $codon; $x++; } } } %IUPAC_DNA = Bio::Tools::IUPAC->iupac_iub(); %IUPAC_AA = Bio::Tools::IUPAC->iupac_iup(); %THREELETTERSYMBOLS = Bio::SeqUtils->valid_aa(2); $VALID_PROTEIN = '['.join('',Bio::SeqUtils->valid_aa(0)).']'; $TERMINATOR = '*';
}
newdescriptionprevnextTop
sub new {
    my($class,@args) = @_;
    my $self = $class->SUPER::new(@args);

    my($id) =
	$self->_rearrange([qw(ID
			     )],
			 @args);

    $id = 1 if ( ! $id );
    $id  && $self->id($id);
    return $self; # success - we hope!
}
iddescriptionprevnextTop
sub id {
   my ($self,$value) = @_;
   if( defined $value) {
       if (  !(defined $TABLES[$value-1]) or $TABLES[$value-1] eq '') {
	   $self->warn("Not a valid codon table ID [$value] ");
	   $value = 0;
       }
       $self->{'id'} = $value;
   }
   return $self->{'id'};
}
namedescriptionprevnextTop
sub name {
   my ($self) = @_;

   my ($id) = $self->{'id'};
   return $NAMES[$id-1];
}
tablesdescriptionprevnextTop
sub tables {
  my %tables;
  for my $id (1 .. @NAMES) {
    my $name = $NAMES[$id-1];
    $tables{$id} = $name if $name;
  }
  return\% tables;
}
translatedescriptionprevnextTop
sub translate {
    my ($self, $seq) = @_;
    $self->throw("Calling translate without a seq argument!") unless defined $seq;
    return '' unless $seq;

    my $id = $self->id;
    my ($partial) = 0;
    $partial = 2 if length($seq) % CODONSIZE == 2;
    
    $seq = lc $seq;
    $seq =~ tr/u/t/;
    my $protein = "";
    if ($seq =~ /[^actg]/ ) { #ambiguous chars
for (my $i = 0; $i < (length($seq) - (CODONSIZE-1)); $i+= CODONSIZE) { my $triplet = substr($seq, $i, CODONSIZE); if( $triplet eq $CODONGAP ) { $protein .= $GAP; } elsif (exists $CODONS->{$triplet}) { $protein .= substr($TABLES[$id-1], $CODONS->{$triplet},1); } else { $protein .= $self->_translate_ambiguous_codon($triplet); } } } else { # simple, strict translation
for (my $i = 0; $i < (length($seq) - (CODONSIZE -1)); $i+=CODONSIZE) { my $triplet = substr($seq, $i, CODONSIZE); if( $triplet eq $CODONGAP ) { $protein .= $GAP; } if (exists $CODONS->{$triplet}) { $protein .= substr($TABLES[$id-1], $CODONS->{$triplet}, 1); } else { $protein .= 'X'; } } } if ($partial == 2) { # 2 overhanging nucleotides
my $triplet = substr($seq, ($partial -4)). "n"; if( $triplet eq $CODONGAP ) { $protein .= $GAP; } elsif (exists $CODONS->{$triplet}) { my $aa = substr($TABLES[$id-1], $CODONS->{$triplet},1); $protein .= $aa; } else { $protein .= $self->_translate_ambiguous_codon($triplet, $partial); } } return $protein;
}
_translate_ambiguous_codondescriptionprevnextTop
sub _translate_ambiguous_codon {
    my ($self, $triplet, $partial) = @_;
    $partial ||= 0;
    my $id = $self->id;
    my $aa;
    my @codons = _unambiquous_codons($triplet);
    my %aas =();
    foreach my $codon (@codons) {
	$aas{substr($TABLES[$id-1],$CODONS->{$codon},1)} = 1;
    }
    my $count = scalar keys %aas;
    if ( $count == 1 ) {
	$aa = (keys %aas)[0];
    }
    elsif ( $count == 2 ) {
	if ($aas{'D'} and $aas{'N'}) {
	    $aa = 'B';
	}
	elsif ($aas{'E'} and $aas{'Q'}) {
	    $aa = 'Z';
	} else {
	    $partial ? ($aa = '') : ($aa = 'X');
	}
    } else {
	$partial ? ($aa = '') :  ($aa = 'X');
    }
    return $aa;
}
translate_strictdescriptionprevnextTop
sub translate_strict {
   my ($self, $value) = @_;
   my ($id) = $self->{'id'};

   $value  = lc $value;
   $value  =~ tr/u/t/;

   if (length $value != 3 ) {
       return '';
   }
   elsif (!(defined $CODONS->{$value}))  {
       return 'X';
   }
   else {
       return substr($TABLES[$id-1],$CODONS->{$value},1);
   }
}
revtranslatedescriptionprevnextTop
sub revtranslate {
    my ($self, $value, $coding) = @_;
    my ($id) = $self->{'id'};
    my (@aas,  $p);
    my (@codons) = ();

    if (length($value) == 3 ) {
	$value = lc $value;
	$value = ucfirst $value;
	$value = $THREELETTERSYMBOLS{$value};
    }
    if ( defined $value and $value =~ /$VALID_PROTEIN/ 
	 and length($value) == 1 ) {
	$value = uc $value;
	@aas = @{$IUPAC_AA{$value}};	
	foreach my $aa (@aas) {
	    #print $aa, " -2\n";
$aa = '\*' if $aa eq '*'; while ($TABLES[$id-1] =~ m/$aa/g) { $p = pos $TABLES[$id-1]; push (@codons, $TRCOL->{--$p}); } } } if ($coding and uc ($coding) eq 'RNA') { for my $i (0..$#codons) { $codons[$i] =~ tr/t/u/; } } return @codons;
}
reverse_translate_alldescriptionprevnextTop
sub reverse_translate_all {
	
	my ($self, $obj, $cut, $threshold) = @_;

    ## check args are OK
if (!$obj || !$obj->isa('Bio::PrimarySeqI')){ $self->throw(" I need a Bio::PrimarySeqI object, not a [". ref($obj) . "]"); } if($obj->alphabet ne 'protein') { $self->throw("Cannot reverse translate, need an amino acid sequence .". "This sequence is of type [" . $obj->alphabet ."]"); } my @data; my @seq = split '', $obj->seq; ## if we're not supplying a codon usage table...
if( !$cut && !$threshold) { ## get lists of possible codons for each aa.
for my $aa (@seq) { if ($aa =~ /x/i) { push @data, (['NNN']); }else { my @cods = $self->revtranslate($aa); push @data,\@ cods; } } }else{ #else we are supplying a codon usage table, we just want common codons
#check args first.
if(!$cut->isa('Bio::CodonUsage::Table')) { $self->throw("I need a Bio::CodonUsage::Table object, not a [". ref($cut). "]."); } my $cod_ref = $cut->probable_codons($threshold); for my $aa (@seq) { if ($aa =~ /x/i) { push @data, (['NNN']); next; } push @data, $cod_ref->{$aa}; } } return $self->_make_iupac_string(\@data);
}
is_start_codondescriptionprevnextTop
sub is_start_codon {
   my ($self, $value) = @_;
   my ($id) = $self->{'id'};

   $value  = lc $value;
   $value  =~ tr/u/t/;

   if (length $value != 3  )  {
       return 0;
   }
   else {
       my $result = 1;
       my @ms = map { substr($STARTS[$id-1],$CODONS->{$_},1) } _unambiquous_codons($value);
       foreach my $c (@ms) {
	   $result = 0 if $c ne 'M';
       }
       return $result;
   }
}
is_ter_codondescriptionprevnextTop
sub is_ter_codon {
   my ($self, $value) = @_;
   my ($id) = $self->{'id'};

   $value  = lc $value;
   $value  =~ tr/u/t/;

   if (length $value != 3  )  {
       return 0;
   }
   else {
       my $result = 1;
       my @ms = map { substr($TABLES[$id-1],$CODONS->{$_},1) } _unambiquous_codons($value);
       foreach my $c (@ms) {
	   $result = 0 if $c ne $TERMINATOR;
       }
       return $result;
   }
}
is_unknown_codondescriptionprevnextTop
sub is_unknown_codon {
   my ($self, $value) = @_;
   my ($id) = $self->{'id'};

   $value  = lc $value;
   $value  =~ tr/u/t/;

   if (length $value != 3  )  {
       return 1;
   }
   else {
       my $result = 0;
       my @cs = map { substr($TABLES[$id-1],$CODONS->{$_},1) } _unambiquous_codons($value);
       $result = 1 if scalar @cs == 0;
       return $result;
   }
}
_unambiquous_codonsdescriptionprevnextTop
sub _unambiquous_codons {
    my ($value) = @_;
    my @nts = ();
    my @codons = ();
    my ($i, $j, $k);
    @nts = map { $IUPAC_DNA{uc $_} }  split(//, $value);
    for my $i (@{$nts[0]}) {
	for my $j (@{$nts[1]}) {
	    for my $k (@{$nts[2]}) {
		push @codons, lc "$i$j$k";
	    }
	}
    }
    return @codons;
}
add_tabledescriptionprevnextTop
sub add_table {
    my ($self, $name, $table, $starts) = @_;

    $name ||= 'Custom'. scalar @NAMES + 1;
    $starts ||= $STARTS[0]; 
    $self->throw('Suspect input!')
        unless length($table) == 64 and length($starts) == 64;

    push @NAMES, $name;
    push @TABLES, $table;
    push @STARTS, $starts;

    return scalar @NAMES;
}
_make_iupac_stringdescriptionprevnextTop
sub _make_iupac_string {
	my ($self, $cod_ref) = @_;
	if(ref($cod_ref) ne 'ARRAY') {
		$self->throw(" I need a reference to a list of references to codons, ".
					 " not a [". ref($cod_ref) . "].");
		}
    my %iupac_hash   = Bio::Tools::IUPAC->iupac_rev_iub();
	my $iupac_string = ''; ## the string to be returned
for my $aa (@$cod_ref) { ## scan through codon positions, record the differing values,
# then look up in the iub hash
for my $index(0..2) { my %h; map { my $k = substr($_,$index,1); $h{$k} = undef;} @$aa; my $lookup_key = join '', sort{$a cmp $b}keys %h; ## extend string
$iupac_string .= $iupac_hash{uc$lookup_key}; } } return $iupac_string;
}
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
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:
  http://bugzilla.open-bio.org/
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 _