[Bioperl-l] Exact codon numbering

Mato Nagel nagel at moldiag.de
Tue Apr 21 14:31:29 UTC 2009


Dear colleagues,
I spend this evening browsing all your information but didn't succeed in 
finding a module that translates feature data (CDS and mRNA) into codon 
numbering.
I developed a routine that from an NCBI xml-file creates a structure
$exonstructure =[ splice_variant_1->[exon_1->{mRNA_from ->'1',
                                                                        
mRNA_to->'something',
                                                                        
cDNA_from->'something',
                                                                        
cDNA_to->'something',
                                                                        
CDS_from->'something',
                                                                        
CDS_to->'something',
                                                                        }

                                                         exon_2->{...}
                                                         ...
                                                         ]
                            splice_variant_2  [... ]
                            ]        
I wonder if it is worth publishing this routine in BioPerl.
Looking forward to receiving an answer.
Sincerely Yours
Mato Nagel




More information about the Bioperl-l mailing list