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

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

NAME

       Bio::LiveSeq::Repeat_Region - Repeat_Region class for LiveSeq

SYNOPSIS

	 # documentation needed

DESCRIPTION

       Class for REPEAT_REGION objects. They consist of a beginlabel, an endlabel (both referring to a LiveSeq DNA object) and a strand.  The
       strand could be 1 (forward strand, default), -1 (reverse strand).

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	 : $intron1=Bio::LiveSeq::Repeat_Region->new(-seq => $objref,
						     -start => $startlabel,
						     -end => $endlabel, -strand => 1);

	 Function: generates a new Bio::LiveSeq::Repeat_Region
	 Returns : reference to a new object of class Repeat_Region
	 Errorcode -1
	 Args	 : two labels and an integer

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

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

NAME

       Bio::LiveSeq::AARange - AARange abstract class for LiveSeq

SYNOPSIS

	 #documentation needed

DESCRIPTION

       This is used as possible parent for aminoacid range object classes.  Or it can be used straight away to define aminoacid ranges.  The idea
       is that the ranges defined are attached to a Translation object and they refer to its coordinate-system when they are first created (via
       the new() method).  When they are created they are anyway linked to the underlying DNA LiveSeq by way of the LiveSeq labels. This allows to
       preserve the ranges even if the numbering changes in the Translation due to deletions or insertions.

       The protein sequence associated with the AARange can be accessed via the usual seq() or subseq() methods.

       The start and end of the AARange in protein coordinate system can be fetched with aa_start() and aa_end() methods. Note: the behaviour of
       these methods would be influenced by the coordinate_start set in the corresponding Translation object. This can be desirable but can also
       lead to confusion if the coordinate_start had been changed and the original position of the AARange was to be retrieved.

       start() and end() methods of the AARange will point to the labels identifying the first nucleotide of the first and last triplet coding for
       the start and end of the AminoAcidRange.

       The underlying nucleotide sequence of the AARange can be retrieved with the labelsubseq() method. This would retrieve the whole DNA
       sequence, including possible introns. This is called "DNA_sequence".

       To fetch the nucleotide sequence of the Transcript, without introns, the labelsubseq() of the attached Transcript (the Transcript the
       Translation comes from) has to be accessed. This is called "cDNA_sequence".

       Here are the operations to retrieve these latter two kinds of sequences:

	  $startlabel=$AARange->start;
	  $endtripletlabel=$AARange->end;
	  $endlabel=$AARange->{'seq'}->label(3,$endtripletlabel,$AARange->strand);

	  $dnaseq=$AARange->labelsubseq($startlabel,undef,$endlabel));

	  $cdnaseq=$AARange->get_Transcript->labelsubseq($startlabel,undef,$endlabel);

       To simplify, these operations have been included in two additional methods: dna_seq() and cdna_seq().

       These would return the whole sequence, as in the examples above.  But the above general scheme can be used by specifying different labels,
       to retrieve hypothetical subsequences of interest.

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	 : $aarange = Bio::LiveSeq::AARange->new(-translation => $obj_ref,
						      -start => $beginaa,
						      -end => $endaa,
						      -name => "ABCD",
						      -description => "DCBA",
						      -translength => $length);

	 Function: generates a new AminoAcidRange LiveSeq object
	 Returns : reference to a new object of class AARange
	 Errorcode -1
	 Args	 : two positions in AminoAcid coordinate numbering
		   an object reference specifying to which translation the aminoacid
		   ranges refer to
		   a name and a description (optional)
		   an optional "translength" argument: this can be given when
		   a lot of AARanges are to be created at the same time for the same
		   Translation object, calculating it with $translation->length
		   This would increase the speed, avoiding the new() function to
		   calculate everytime the same length again and again for every obj.

   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

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

   aa_start
	 Title	 : aa_start
	 Usage	 : $end = $aarange->aa_start()
	 Returns : integer (position, according to Translation coordinate system) of
		   the start of an AminoAcidRange object
	 Args	 : none

   aa_end
	 Title	 : aa_end
	 Usage	 : $end = $aarange->aa_end()
	 Returns : integer (position, according to Translation coordinate system) of
		   the end of an AminoAcidRange object
	 Args	 : none

   dna_seq
	 Title	 : dna_seq
	 Usage	 : $end = $aarange->dna_seq()
	 Returns : the sequence at DNA level of the entire AminoAcidRange
		   this would include introns (if present)
	 Args	 : none

   cdna_seq
	 Title	 : cdna_seq
	 Usage	 : $end = $aarange->cdna_seq()
	 Returns : the sequence at cDNA level of the entire AminoAcidRange
		   i.e. this is the part of the Transcript that codes for the
		   AminoAcidRange. It would be composed just of exonic DNA.
	 Args	 : none

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