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