SYNOPSIS
use Bio::PrimarySeq;
use Bio::Tools::IUPAC;
# Get the IUPAC code for proteins
my %iupac_prot = Bio::Tools::IUPAC->new->iupac_iup;
# Create a sequence with degenerate residues
my $ambiseq = Bio::PrimarySeq->new(-seq => 'ARTCGUTGN', -alphabet => 'dna');
# Create all possible non-degenerate sequences
my $iupac = Bio::Tools::IUPAC->new(-seq => $ambiseq);
while ($uniqueseq = $iupac->next_seq()) {
# process the unique Bio::Seq object.
}
# Get a regular expression that matches all possible sequences
my $regexp = $iupac->regexp();
DESCRIPTION
Bio::Tools::IUPAC is a tool that manipulates sequences with ambiguous residues following the IUPAC conventions. Non-standard characters have the meaning described below:
IUPAC-IUB SYMBOLS FOR NUCLEOTIDE (DNA OR RNA) NOMENCLATURE:
Cornish-Bowden (1985) Nucl. Acids Res. 13: 3021-3030
---------------------------------------------------------------
Symbol Meaning Nucleic Acid
---------------------------------------------------------------
A A Adenine
C C Cytosine
G G Guanine
T T Thymine
U U Uracil
M A or C aMino
R A or G puRine
W A or T Weak
S C or G Strong
Y C or T pYrimidine
K G or T Keto
V A or C or G not T (closest unused char after T)
H A or C or T not G (closest unused char after G)
D A or G or T not C (closest unused char after C)
B C or G or T not A (closest unused char after A)
X G or A or T or C Unknown (very rarely used)
N G or A or T or C Unknown (commonly used)
IUPAC-IUP AMINO ACID SYMBOLS:
Biochem J. 1984 Apr 15; 219(2): 345-373
Eur J Biochem. 1993 Apr 1; 213(1): 2
------------------------------------------
Symbol Meaning
------------------------------------------
A Alanine
B Aspartic Acid, Asparagine
C Cysteine
D Aspartic Acid
E Glutamic Acid
F Phenylalanine
G Glycine
H Histidine
I Isoleucine
J Isoleucine/Leucine
K Lysine
L Leucine
M Methionine
N Asparagine
O Pyrrolysine
P Proline
Q Glutamine
R Arginine
S Serine
T Threonine
U Selenocysteine
V Valine
W Tryptophan
X Unknown
Y Tyrosine
Z Glutamic Acid, Glutamine
* Terminator
There are a few things Bio::Tools::IUPAC can do for you:
- report the IUPAC mapping between ambiguous and non-ambiguous residues
- produce a stream of all possible corresponding unambiguous Bio::Seq objects given an ambiguous sequence object
- convert an ambiguous sequence object to a corresponding regular expression
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.
[email protected] - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list: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/issues
AUTHOR - Aaron Mackey
Email amackey-at-virginia.eduAPPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _new
Title : new
Usage : Bio::Tools::IUPAC->new($seq);
Function: Create a new IUPAC object, which acts as a sequence stream (akin to
SeqIO)
Args : an ambiguously coded sequence object that has a specified 'alphabet'
Returns : a Bio::Tools::IUPAC object.
next_seq
Title : next_seq Usage : $iupac->next_seq(); Function: returns the next unique sequence object Args : none. Returns : a Bio::Seq object
iupac
Title : iupac
Usage : my %symbols = $iupac->iupac;
Function: Returns a hash of symbols -> symbol components of the right type
for the given sequence, i.e. it is the same as iupac_iup() if
Bio::Tools::IUPAC was given a proteic sequence, or iupac_iub() if the
sequence was nucleic. For example, the key 'M' has the value ['A', 'C'].
Args : none
Returns : Hash
iupac_amb
Title : iupac_amb
Usage : my %symbols = $iupac->iupac_amb;
Function: Same as iupac() but only contains a mapping between ambiguous residues
and the ambiguous residues they map to. For example, the key 'N' has
the value ['R', 'Y', 'K', 'M', 'S', 'W', 'B', 'D', 'H', 'V', 'N'],
i.e. it matches all other ambiguous residues.
Args : none
Returns : Hash
iupac_iup
Title : iupac_iup Usage : my %aasymbols = $iupac->iupac_iup; Function: Returns a hash of PROTEIN symbols -> non-ambiguous symbol components Args : none Returns : Hash
iupac_iup_amb
Title : iupac_iup_amb Usage : my %aasymbols = $iupac->iupac_iup_amb; Function: Returns a hash of PROTEIN symbols -> ambiguous symbol components Args : none Returns : Hash
iupac_iub
Title : iupac_iub Usage : my %dnasymbols = $iupac->iupac_iub; Function: Returns a hash of DNA symbols -> non-ambiguous symbol components Args : none Returns : Hash
iupac_iub_amb
Title : iupac_iub_amb Usage : my %dnasymbols = $iupac->iupac_iub; Function: Returns a hash of DNA symbols -> ambiguous symbol components Args : none Returns : Hash
iupac_rev_iub
Title : iupac_rev_iub
Usage : my %dnasymbols = $iupac->iupac_rev_iub;
Function: Returns a hash of nucleotide combinations -> IUPAC code
(a reverse of the iupac_iub hash).
Args : none
Returns : Hash
count
Title : count
Usage : my $total = $iupac->count();
Function: Calculates the number of unique, unambiguous sequences that
this ambiguous sequence could generate
Args : none
Return : int
regexp
Title : regexp
Usage : my $re = $iupac->regexp();
Function: Converts the ambiguous sequence into a regular expression that
matches all of the corresponding ambiguous and non-ambiguous sequences.
You can further manipulate the resulting regular expression with the
Bio::Tools::SeqPattern module. After you are done building your
regular expression, you might want to compile it and make it case-
insensitive:
$re = qr/$re/i;
Args : 1 to match RNA: T and U characters will match interchangeably
Return : regular expression