[Bioperl-l] Parseing tRNA sequences out of genbank file

Adam Witney awitney at sghms.ac.uk
Tue Feb 1 07:38:43 EST 2005


I am parsing a genbank file and it contains an entry like so...

     tRNA            complement(1326335..1326419)
                     /product="transfer RNA-Leu"
                     /note="tRNA Leu anticodon CAA, Cove score 51.10"

However this code

      if($feat->primary_tag eq 'tRNA')
          my $seq_obj = $feat->seq;
          my $gene_length = length($seq_obj->seq);

I get this error

------------- EXCEPTION  -------------
MSG: Sequence is a protein. Cannot revcom
STACK Bio::PrimarySeqI::revcom
STACK Bio::SeqFeature::Generic::seq
STACK toplevel ../../1.0b1/sql/scripts/gene_upload.pl:379


I am trying to get the DNA sequence corresponding to the tRNA, why does it
think it is a protein sequence? It works fine for tRNA's which aren't on the
reverse strand

Thanks for any help


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