Bio::Tools::IUPAC(3) User Contributed Perl Documentation Bio::Tools::IUPAC(3)NAMEBio::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
perl v5.14.1 2011-07-22 Bio::Tools::IUPAC(3)
