Bio::LiveSeq::Transcript - Transcript class for LiveSeq # documentation needed This stores informations about coding sequences (CDS). The implementation is that a Transcript object accesses a collection of Exon objects, inferring from them the nucleotide structure and sequence. Email: Insana@ebi.ac.uk, jinsana@gmx.net Address: EMBL Outstation, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambs. CB10 1SD, United Kingdom The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
Title : new Usage : $transcript = Bio::LiveSeq::Transcript->new(-exons => \@obj_refs); Function: generates a new Bio::LiveSeq::Transcript Returns : reference to a new object of class Transcript Errorcode -1 Args : reference to an array of Exon object references

all_Exons
Title : all_Exons Usage : $transcript_obj->all_Exons() Function: returns references to all Exon objects the Transcript is composed of Example : foreach $exon ($transcript->all_Exons()) { do_something } Returns : array of object references Args : none

downstream_seq
Title : downstream_seq Usage : $transcript_obj->downstream_seq() : $transcript_obj->downstream_seq(64) Function: returns a string of nucleotides downstream of the end of the CDS. If there is some information of the real mRNA, from features in an attached Gene object, it will return up to those boundaries. Otherwise it will return 1000 nucleotides. If an argument is given it will override the default 1000 number and return instead /that/ requested number of nucleotides. But if a Gene object is attached, this argument will be ignored. Returns : string Args : an optional integer number of nucleotides to be returned instead of the default if no gene attached

upstream_seq
Title : upstream_seq Usage : $transcript_obj->upstream_seq() : $transcript_obj->upstream_seq(64) Function: just like downstream_seq but returns nucleotides before the ATG Note : the default, if no Gene information present and no nucleotides number given, is to return up to 400 nucleotides.

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

translation_table
Title : translation_table Usage : $name = $obj->translation_table; : $name = $obj->translation_table(11); Function: Returns or sets the translation_table used for translating the transcript. If it has never been set, it will return undef. Returns : an integer

frame
Title : frame Usage : $frame = $transcript->frame($label); Function: Returns the frame of a particular nucleotide. Frame can be 0 1 or 2 and means the position in the codon triplet of the particulat nucleotide. 0 is the first codon_position. Codon_position (1 2 3) is simply frame+1. If the label asked for is not inside the Transcript, -1 will be returned. Args : a label Returns : 0 1 or 2 Errorcode -1