[Bioperl-l] Question on SeqFeature_RelationShip

lajus florian.lajus at inria.fr
Tue Jan 10 12:06:31 EST 2012


Hello,
I am currently working on a refactoring of the Genolevures project 
(http://www.genolevures.org/)
We are trying to better use bioperl and the bioSQL shema on a postgreSQL 
database.

I have loaded an EMBL file into my BioSQL database (postgres). If I look 
in my database, my bioentry have been added and seqFeatures associated too.
But it seems that my seqfeature_relationship table is empty.
I find it strange in so far as there is a relationship between gene and 
its CDS. right?
example: (extract of my EMBL file)

FT   gene <30978..>32507
FT                   /locus_tag="CAGL0A00319g"
FT                   /old_locus_tag="CAGL-IPF3315"
FT                   /old_locus_tag="CAGL-CDS2015.1"
FT   CDS             30978..32507
FT                   /locus_tag="CAGL0A00319g"
FT                   /old_locus_tag="CAGL-IPF3315"
FT                   /old_locus_tag="CAGL-CDS2015.1"
FT                   /note="similar to uniprot|P16639 Saccharomyces 
cerevisiae
FT                   YGL017w ATE1 arginyl tRNA transferase"
FT                   /db_xref="GOA:Q6FXV3"
FT                   /db_xref="InterPro:IPR007471"
FT                   /db_xref="InterPro:IPR007472"
FT                   /db_xref="InterPro:IPR016181"
FT                   /db_xref="InterPro:IPR017137"
FT                   /db_xref="UniProtKB/TrEMBL:Q6FXV3"
FT                   /inference="similar to AA sequence:UniProtKB:P16639"
FT                   /protein_id="CAG57677.1"
FT                   
/translation="MENKLIIHRPLYFSDKSDCGYCHGKKAKGSDFYSLESWYERIKEN
FT                   
ADSEVEELPVRSCTVGFQCENMTVAMYDQMCNMGFRRSGLFVYKMDALRSCCRLYTIRT
FT                   
RPDWFKLTKDMRKCINRFRKHVLGEPVANAKTQGYVEDIVDIEGQSDSINFYTRFGPAV
FT                   
YTDEKYELFSIYQERVHQDFDHSKKGFKRFLCDAPFTQGVIMGTEEEWEQLNNWKSMKP
FT                   
GERLLRTGPVHESYYYKGKLIALAVTDFLPSGISSVYFIWHPDYHKWSLGKLSALRELS
FT                   
LVSKTNLKYYYLGYYIDDCKKMNYKANYGGELLDSCTERYFKLSQVKDMIRGGKLFMVG
FT                   
TQGHDISREVALSDAIRDCIYQTDAFDIASDDNVAEKVYGTSSNIYRPQYLKEVISFLK
FT                   
TSGLEYDFPIYNDGVFNQYAKRIAKDGEDPDFTIPSICPGLIPLWELKDLLMSGKLQKE
FT                   LTGRTLVFDTSFGFIRKLEPWEDEDSTTKTAICDVVRLLGLEMASNSIVVV"

you can find the entire EMBL file here : 
http://www.ebi.ac.uk/htbin/expasyfetch?CR380947

For us, it exists a relationship between the gene and its CDS. So why is 
the table seqfeature_relationship table empty?
Have we missed something?

PS: Sorry for my bad english...

Lajus Florian.




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