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Bio::Tools::IUPAC.3pm
Langue: en
Version: 2010-05-19 (ubuntu - 24/10/10)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Tools::IUPAC - Generates unique Seq objects from an ambiguous Seq objectSYNOPSIS
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.
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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
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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.eduAPPENDIX
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
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre