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

[Venky Nandagopal]

Lincoln,

Thanks for responding. Scott McCain helped me resolve this problem, which 
was indeed some sort of strange database error. I dropped and reloaded the 
database and that fixed it.

Venky



On Wed, 16 Jul 2003 12:55:45 -0400, Lincoln Stein <lstein at cshl.edu> wrote:

> 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
>



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