/ 
BioPerl-1.6.901
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Tools::IUPAC

NAME

Bio::Tools::IUPAC - Generates unique Seq objects from an ambiguous Seq object

SYNOPSIS

use Bio::Seq;
use Bio::Tools::IUPAC;

my $ambiseq = Bio::Seq->new(-seq => 'ARTCGUTGR', -alphabet => 'dna');
my $stream  = Bio::Tools::IUPAC->new(-seq => $ambiseq);

while ($uniqueseq = $stream->next_seq()) {
    # process the unique Seq object.
}

DESCRIPTION

IUPAC is a tool that produces a stream of unique, "strict"-satisfying Seq objects from an ambiquous Seq object (containing non-standard characters given the meaning shown below)

Extended DNA / RNA alphabet :
(includes symbols for nucleotide ambiguity)
------------------------------------------
Symbol       Meaning      Nucleic Acid
------------------------------------------
 A            A           Adenine
 C            C           Cytosine
 G            G           Guanine
 T            T           Thymine
 U            U           Uracil
 M          A or C
 R          A or G
 W          A or T
 S          C or G
 Y          C or T
 K          G or T
 V        A or C or G
 H        A or C or T
 D        A or G or T
 B        C or G or T
 X      G or A or T or C
 N      G or A or T or C

IUPAC-IUB SYMBOLS FOR NUCLEOTIDE NOMENCLATURE:
  Cornish-Bowden (1985) Nucl. Acids Res. 13: 3021-3030.

-----------------------------------

Amino Acid alphabet:
 ------------------------------------------
 Symbol           Meaning
 ------------------------------------------
 A        Alanine
 B        Aspartic Acid, Asparagine
 C        Cystine
 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


 IUPAC-IUP AMINO ACID SYMBOLS:
   Biochem J. 1984 Apr 15; 219(2): 345-373
   Eur J Biochem. 1993 Apr 1; 213(1): 2

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://redmine.open-bio.org/projects/bioperl/

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: returns a new seq stream (akin to SeqIO)
Returns : a Bio::Tools::IUPAC stream object that will produce unique
          Seq objects on demand.
Args    : an ambiguously coded Seq.pm object that has a specified 'alphabet'

next_seq

Title   : next_seq
Usage   : $iupac->next_seq()
Function: returns the next unique Seq object
Returns : a Seq.pm object
Args    : none.

iupac_iup

Title   : iupac_iup
Usage   : my %aasymbols = $iupac->iupac_iup
Function: Returns a hash of PROTEIN symbols -> symbol components
Returns : Hash
Args    : none

iupac_iub

Title   : iupac_iub
Usage   : my %dnasymbols = $iupac->iupac_iub
Function: Returns a hash of DNA symbols -> symbol components
Returns : Hash
Args    : none

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).
Returns : Hash
Args    : none

count

Title   : count
Usage   : my $total = $iupac->count();
Function: Calculates the number of unique, unambiguous sequences that
          this ambiguous sequence could generate
Return  : int
Args    : none