1Bio::Tools::CodonTable(U3s)er Contributed Perl DocumentatBiioon::Tools::CodonTable(3)
2
6 Bio::Tools::CodonTable - Bioperl codon table object
7
9 # This is a read-only class for all known codon tables. The IDs are
10 # the ones used by nucleotide sequence databases. All common IUPAC
11 # ambiguity codes for DNA, RNA and animo acids are recognized.
12 # to use
14 use Bio::Tools::CodonTable;
15 # defaults to ID 1 "Standard"
17 $myCodonTable = Bio::Tools::CodonTable->new();
18 $myCodonTable2 = Bio::Tools::CodonTable->new( -id => 3 );
19 # change codon table
21 $myCodonTable->id(5);
22 # examine codon table
24 print join (' ', "The name of the codon table no.", $myCodonTable->id(4),
25 "is:", $myCodonTable->name(), "\n");
26 # print possible codon tables
28 $tables = Bio::Tools::CodonTable->tables;
29 while ( ($id,$name) = each %{$tables} ) {
30 print "$id = $name\n";
31 }
32 # translate a codon
34 $aa = $myCodonTable->translate('ACU');
35 $aa = $myCodonTable->translate('act');
36 $aa = $myCodonTable->translate('ytr');
37 # reverse translate an amino acid
39 @codons = $myCodonTable->revtranslate('A');
40 @codons = $myCodonTable->revtranslate('Ser');
41 @codons = $myCodonTable->revtranslate('Glx');
42 @codons = $myCodonTable->revtranslate('cYS', 'rna');
43 # reverse translate an entire amino acid sequence into a IUPAC
45 # nucleotide string
46 my $seqobj = Bio::PrimarySeq->new(-seq => 'FHGERHEL');
48 my $iupac_str = $myCodonTable->reverse_translate_all($seqobj);
49 #boolean tests
51 print "Is a start\n" if $myCodonTable->is_start_codon('ATG');
52 print "Is a termianator\n" if $myCodonTable->is_ter_codon('tar');
53 print "Is a unknown\n" if $myCodonTable->is_unknown_codon('JTG');
54
56 Codon tables are also called translation tables or genetic codes since
57 that is what they represent. A bit more complete picture of the full
58 complexity of codon usage in various taxonomic groups is presented at
59 the NCBI Genetic Codes Home page.
60 CodonTable is a BioPerl class that knows all current translation tables
62 that are used by primary nucleotide sequence databases (GenBank, EMBL
63 and DDBJ). It provides methods to output information about tables and
64 relationships between codons and amino acids.
65 This class and its methods recognized all common IUPAC ambiguity codes
67 for DNA, RNA and animo acids. The translation method follows the con‐
68 ventions in EMBL and TREMBL databases.
69 It is a nuisance to separate RNA and cDNA representations of nucleic
71 acid transcripts. The CodonTable object accepts codons of both type as
72 input and allows the user to set the mode for output when reverse
73 translating. Its default for output is DNA.
74 Note:
76 This class deals primarily with individual codons and amino acids. How‐
78 ever in the interest of speed you can translate longer sequence, too.
79 The full complexity of protein translation is tackled by Bio::Primary‐
80 SeqI::translate.
81 The amino acid codes are IUPAC recommendations for common amino acids:
83 A Ala Alanine
85 R Arg Arginine
86 N Asn Asparagine
87 D Asp Aspartic acid
88 C Cys Cysteine
89 Q Gln Glutamine
90 E Glu Glutamic acid
91 G Gly Glycine
92 H His Histidine
93 I Ile Isoleucine
94 L Leu Leucine
95 K Lys Lysine
96 M Met Methionine
97 F Phe Phenylalanine
98 P Pro Proline
99 O Pyl Pyrrolysine (22nd amino acid)
100 U Sec Selenocysteine (21st amino acid)
101 S Ser Serine
102 T Thr Threonine
103 W Trp Tryptophan
104 Y Tyr Tyrosine
105 V Val Valine
106 B Asx Aspartic acid or Asparagine
107 Z Glx Glutamine or Glutamic acid
108 J Xle Isoleucine or Valine (mass spec ambiguity)
109 X Xaa Any or unknown amino acid
110 It is worth noting that, "Bacterial" codon table no. 11 produces an
112 polypeptide that is, confusingly, identical to the standard one. The
113 only differences are in available initiator codons.
114 NCBI Genetic Codes home page:
116 http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c
117 EBI Translation Table Viewer:
119 http://www.ebi.ac.uk/cgi-bin/mutations/trtables.cgi
120 Amended ASN.1 version with ids 16 and 21 is at:
122 ftp://ftp.ebi.ac.uk/pub/databases/geneticcode/
123 Thanks to Matteo diTomasso for the original Perl implementation of
125 these tables.
126
128 Mailing Lists
129 User feedback is an integral part of the evolution of this and other
131 Bioperl modules. Send your comments and suggestions preferably to the
132 Bioperl mailing lists Your participation is much appreciated.
133 bioperl-l@bioperl.org - General discussion
135 http://bioperl.org/wiki/Mailing_lists - About the mailing lists
136 Reporting Bugs
138 Report bugs to the Bioperl bug tracking system to help us keep track
140 the bugs and their resolution. Bug reports can be submitted via the
141 web:
142 http://bugzilla.open-bio.org/
144
146 Email: heikki-at-bioperl-dot-org
147
149 The rest of the documentation details each of the object methods.
150 Internal methods are usually preceded with a _
151 id
153 Title : id
155 Usage : $obj->id(3); $id_integer = $obj->id();
156 Function:
157 Sets or returns the id of the translation table. IDs are
159 integers from 1 to 15, excluding 7 and 8 which have been
160 removed as redundant. If an invalid ID is given the method
161 returns 0, false.
162 Example :
164 Returns : value of id, a scalar, 0 if not a valid
165 Args : newvalue (optional)
166 name
168 Title : name
170 Usage : $obj->name()
171 Function: returns the descriptive name of the translation table
172 Example :
173 Returns : A string
174 Args : None
175 tables
177 Title : tables
179 Usage : $obj->tables() or Bio::Tools::CodonTable->tables()
180 Function: returns a hash reference where each key is a valid codon
181 table id() number, and each value is the corresponding
182 codon table name() string
183 Example :
184 Returns : A hashref
185 Args : None
186 translate
188 Title : translate
190 Usage : $obj->translate('YTR')
191 Function: Returns a string of one letter amino acid codes from
192 nucleotide sequence input. The imput can be of any length.
193 Returns 'X' for unknown codons and codons that code for
195 more than one amino acid. Returns an empty string if input
196 is not three characters long. Exceptions for these are:
197 - IUPAC amino acid code B for Aspartic Acid and
199 Asparagine, is used.
200 - IUPAC amino acid code Z for Glutamic Acid, Glutamine is
201 used.
202 - if the codon is two nucleotides long and if by adding
203 an a third character 'N', it codes for a single amino
204 acid (with exceptions above), return that, otherwise
205 return empty string.
206 Returns empty string for other input strings that are not
208 three characters long.
209 Example :
211 Returns : a string of one letter ambiguous IUPAC amino acid codes
212 Args : ambiguous IUPAC nucleotide string
213 translate_strict
215 Title : translate_strict
217 Usage : $obj->translate_strict('ACT')
218 Function: returns one letter amino acid code for a codon input
219 Fast and simple translation. User is responsible to resolve
221 ambiguous nucleotide codes before calling this
222 method. Returns 'X' for unknown codons and an empty string
223 for input strings that are not three characters long.
224 It is not recommended to use this method in a production
226 environment. Use method translate, instead.
227 Example :
229 Returns : A string
230 Args : a codon = a three nucleotide character string
231 revtranslate
233 Title : revtranslate
235 Usage : $obj->revtranslate('G')
236 Function: returns codons for an amino acid
237 Returns an empty string for unknown amino acid
239 codes. Ambiquous IUPAC codes Asx,B, (Asp,D; Asn,N) and
240 Glx,Z (Glu,E; Gln,Q) are resolved. Both single and three
241 letter amino acid codes are accepted. '*' and 'Ter' are
242 used for terminator.
243 By default, the output codons are shown in DNA. If the
245 output is needed in RNA (tr/t/u/), add a second argument
246 'RNA'.
247 Example : $obj->revtranslate('Gly', 'RNA')
249 Returns : An array of three lower case letter strings i.e. codons
250 Args : amino acid, 'RNA'
251 is_start_codon
253 Title : is_start_codon
255 Usage : $obj->is_start_codon('ATG')
256 Function: returns true (1) for all codons that can be used as a
257 translation start, false (0) for others.
258 Example : $myCodonTable->is_start_codon('ATG')
259 Returns : boolean
260 Args : codon
261 is_ter_codon
263 Title : is_ter_codon
265 Usage : $obj->is_ter_codon('GAA')
266 Function: returns true (1) for all codons that can be used as a
267 translation tarminator, false (0) for others.
268 Example : $myCodonTable->is_ter_codon('ATG')
269 Returns : boolean
270 Args : codon
271 is_unknown_codon
273 Title : is_unknown_codon
275 Usage : $obj->is_unknown_codon('GAJ')
276 Function: returns false (0) for all codons that are valid,
277 true (1) for others.
278 Example : $myCodonTable->is_unknown_codon('NTG')
279 Returns : boolean
280 Args : codon
281 _unambiquous_codons
283 Title : _unambiquous_codons
285 Usage : @codons = _unambiquous_codons('ACN')
286 Function:
287 Example :
288 Returns : array of strings (one letter unambiguous amino acid codes)
289 Args : a codon = a three IUPAC nucleotide character string
290 add_table
292 Title : add_table
294 Usage : $newid = $ct->add_table($name, $table, $starts)
295 Function: Add a custom Codon Table into the object.
296 Know what you are doing, only the length of
297 the argument strings is checked!
298 Returns : the id of the new codon table
299 Args : name, a string, optional (can be empty)
300 table, a string of 64 characters
301 startcodons, a string of 64 characters, defaults to standard
302perl v5.8.8 2007-05-07 Bio::Tools::CodonTable(3)