[Bioperl-l] Bio::DB::GFF trouble + Blast question

[Venky Nandagopal]

Hi,

I have a couple of problems: (1) I use a database created using 
process_gadfly.pl to access the D.mel genome, via Bio::DB::GFF. I have a 
utility script that returns the sequence of a gene given the CG number, 
using 	@genes = get_feature_by_name(CG####); 	print $genes[0]->seq;
This script seems to work fine for most CG numbers, except for CG6667, 
which is the ID for the dorsal gene. For some reason, no sequence is 
returned by the seq() method. The gene object is not undefined though, 
since $genes[0]->asString returns "gene:gadfly(CG6667)"; similarly the 
start, end, strand methods work fine. I have tried getting transcripts 
instead of the gene etc etc, but CG6667 refuses to yield any sequence. Can 
anyone provide an explanation for this?


(2) This is not directly connect to Bioperl, but BLAST reports sometimes 
provide Expect values in the form "Expect(3)=0.0". What does the 3 refer 
to? Sometimes it says "Expect(7+)=1e-23".


Thanks
Venky


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