/ 
BioPerl-1.007000
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Tools::IUPAC

NAME

Bio::Tools::IUPAC - Generates unique sequence objects or regular expressions from an ambiguous IUPAC sequence

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.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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/issues

AUTHOR - Aaron Mackey

Email amackey-at-virginia.edu

APPENDIX

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