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

[Lincoln Stein]

Hi,

The problem with the dorsal gene would happen if the FASTA files that are you 
loading are out of synch with the feature files.  Can you confirm that you 
are loading all the D.mel FASTA-format files and that they went into the 
database correctly?

One way to confirm this would be to look up the coordinates of the dorsal gene 
manually (grep through the GFF file), and to record three bits of 
information:

		reference sequence, start, end

Then open up the mysql database from the command line and run this query:

	mysql> select * from fdna where fref=$reference 
		AND foffset >=$start AND foffset<=$end;

replace $reference,$start and $end with the values you looked up earlier.

Lincoln

On Thursday 03 July 2003 04:43 am, Venky Nandagopal wrote:
> 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

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
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