Linux Certif

Toute la documentation sur la certification Linux LPI

Bio::Tools::IUPAC.3pm

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:

   http://bugzilla.open-bio.org/
 
 

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