bio::liveseq::dna(3pm) [debian man page]

Bio::LiveSeq::DNA(3pm)					User Contributed Perl Documentation				    Bio::LiveSeq::DNA(3pm)

NAME

       Bio::LiveSeq::DNA - DNA object for LiveSeq

SYNOPSIS

	 # documentation needed

DESCRIPTION

       This holds the DNA sequence (or the RNA in the case of cDNA entries) and is accessed by exons, genes, transcripts... objects

AUTHOR - Joseph A.L. Insana
       Email:  Insana@ebi.ac.uk, jinsana@gmx.net

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

   new
	 Title	 : new
	 Usage	 : $dna = Bio::LiveSeq::DNA->new(-seq => "atcgaccaatggacctca",
						 -offset => 3 );

	 Function: generates a new Bio::LiveSeq::DNA
	 Returns : reference to a new object of class DNA
	 Errorcode -1
	 Args	 : a string
	       AND an optional offset to create nucleotide labels (default is 1, i.e.
		   starting the count of labels from "1") -> do not bother using it ->
		   it could be used by alternative loaders !EMBL format
	 NOTE	 : strand of DNA is set to 1 by default

perl v5.14.2							    2012-03-02						    Bio::LiveSeq::DNA(3pm)

Bio::LiveSeq::Translation(3pm)				User Contributed Perl Documentation			    Bio::LiveSeq::Translation(3pm)

NAME

       Bio::LiveSeq::Translation - Translation class for LiveSeq

SYNOPSIS

	 #documentation needed

DESCRIPTION

       This stores information about aminoacids translations of transcripts.  The implementation is that a Translation object is the translation
       of a Transcript object, with different possibilities of manipulation, different coordinate system and eventually its own ranges (protein
       domains).

AUTHOR - Joseph A.L. Insana
       Email:  Insana@ebi.ac.uk, jinsana@gmx.net

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

   new
	 Title	 : new
	 Usage	 : $protein = Bio::LiveSeq::Translation->new(-transcript => $transcr);

	 Function: generates a new Bio::LiveSeq::Translation
	 Returns : reference to a new object of class Translation
	 Errorcode -1
	 Args	 : reference to an object of class Transcript

   get_Transcript
	 Title	 : valid
	 Usage	 : $transcript = $obj->get_Transcript()
	 Function: retrieves the reference to the object of class Transcript (if any)
		   attached to a LiveSeq object
	 Returns : object reference
	 Args	 : none

   aa_ranges
	 Title	 : aa_ranges
	 Usage	 : @proteinfeatures = $translation->aa_ranges()
	 Function: to retrieve all the LiveSeq AARange objects attached to a
		   Translation, usually created out of a SwissProt database entry
		   crossreferenced from an EMBL CDS feature.
	 Returns : an array
	 Args	 : none

perl v5.14.2							    2012-03-02					    Bio::LiveSeq::Translation(3pm)