[Gusdev-gusdev] LoadPfam doubts

[sucheta T. <su...@vb...>]

Hi,

I was using Loadpfam module and could not detect where the sequence
alignment goes.

Can anyone answer this.

Thanks

Sucheta

> Paul, I see what you mean. Thanks for taking
> time out to shed light on this.
>
> Happy holidays,
>
> Terry
>
> On  0, Pjm <pj...@sa...> wrote:
>> Hi Chetna, Terry,
>>
>> I dunno if this has already been answered. Apologies if so.
>>
>> The Pfam-A.full file I used has duplicate entries which is quite normal.
>> In
>> this cut down example you can see two database references to the same
>> protein but the numbers following it are different;
>>
>> 	# STOCKHOLM 1.0
>> 	#=GF ID   Acyl_CoA_thio
>> 	.
>> 	.
>> 	#=GF DR   PDB; 1c8u A; 147; 281;
>> 	#=GF DR   PDB; 1c8u B; 147; 281;
>> 	#=GF DR   PDB; 1c8u A; 17; 115;
>> 	#=GF DR   PDB; 1c8u B; 17; 115;
>>
>> The numbers are the co-ords on the protein that match up to PF02551.
>> Because the code tries to create another DoTS.DbRefPfamEntry for both of
>> these entries it gives a warning for each.
>>
>> 	Duplicate reference to db_ref_id 1351 from pfam_entry_id 91
>> 	Duplicate reference to db_ref_id 1352 from pfam_entry_id 91
>>
>> Does this help?
>> Paul.
>>
>> Chetna Warade wrote:
>> >Hello Terry,
>> >
>> >Thanks for the log. I am looking at it and observed
>> >that the pfam_entry_id in your log is a continous
>> >number from the log whereas for me its different.
>> >
>> >Thanks again,
>> >Chetna
>> >
>> >--- Terry Clark <tw...@cs...> wrote:
>> >
>> >>Hi, Chetna,
>> >>I also experienced numerous duplicate entries in the
>> >>pfam load.
>> >>I assumed these were problems with Pfam
>> >>organization, and not
>> >>being a priority to me, I did not track them down;
>> >>but I have
>> >>a not in my log to do so. I've attached my Pfam load
>> >>output
>> >>for comparison.
>> >>
>> >>Terry
>> >>
>> >>
>> >>
>> >>On  0, Chetna Warade <wa...@ya...> wrote:
>> >>
>> >>>Hello Debbie,
>> >>>
>> >>>I am loading (commit) Pfam data  in GUS from
>> >>
>> >>scratch.
>> >>
>> >>>I am getting few duplicate errors e.g.
>> >>>
>> >>>Duplicate reference to db_ref_id 621 from
>> >>>pfam_entry_id 1073
>> >>>
>> >>>Is this behavior okey? If not do you have any idea
>> >>>about  fixes for this.
>> >>>
>> >>>Thanks in advance,
>> >>>Chetna
>> >>>
>> >
>> >
>> >
>> >
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-- 
Sucheta Tripathy
Virginia Bioinformatics Institute
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