[BioSQL-l] Relationship between Gene CDS and mRNA Seqfeatures

[Nicholas Thrower]

Peter,

Thank you for the quick answer.

Yes, I used the BioPerl wrapper to load the data.

I was interested in using BioRuby but was not able to find ruby scripts
comparable to load_ncbi_taxonomy.pl and load_seqdatabase.pl.

-Nick


On 11/3/10 12:20 PM, "Peter" <biopython at maubp.freeserve.co.uk> wrote:

> On Wed, Nov 3, 2010 at 3:49 PM, Nicholas Thrower <throwern at msu.edu> wrote:
>> 
>> Hello all,
>> 
>> I¹m new to this list so I hope this question hasn¹t been asked before. I
>> couldn¹t find an archive to search.
>> 
>> I have a biosql schema in oracle loaded with several genbank entries
>> including TAIR9. I would like some help determining the relationship between
>> mrna and cds features that belong to a single Gene entry.
>> 
>> My seqfeature table has the following entries.
>> 
>> OID         RANK    DISPLAY_NAME    ENT_OID     TYPE_TRM_OID
>> SOURCE_TRM_OID
>> 666269  22747   Gene                       643516        626447
>> 626431
>> 666270  22748   Mrna                       643516        626451
>> 626431
>> 666271  22749   Mrna                       643516        626451
>> 626431
>> 666272  22750   Cds                          643516        626455
>> 626431
>> 666273  22751   Cds                          643516        626455
>> 626431
>> 
>> I¹m trying to correlate CDS to mRNA so that I can display them. All of the
>> seqfeatures have the same exact locus_tag qualifier and I can¹t find any
>> other qualifiers noting this relationship. Do I need to make an assumption
>> based on seqfeature id, or rank in order to determine the relationship
>> between mRNA and CDS.
>> 
>> Here is an example from TAIR of what this data could look like.
>> http://arabidopsis.org/servlets/TairObject?id=134549&type=locus
>> 
>> How do I know which CDS and mRNA are paired together?
>> 
>> -Nick
> 
> In a GenBank file this relationship between CDS and mRNA or gene
> features is implicit from the order in the file. I think the rank is used in
> BioSQL to record the feature order, so you'd have to look at that.
> (This is assuming the Bio* wrapper you used to load the GenBank
> file into BioSQL isn't making any inferences like this for you).
> 
> P.S. Which Bio* wrapper are you using? BioPerl?
> 
> Peter