[BiO BB] difference between Refseq and Uniprot

[Dan Bolser]

When it comes to redundancy its good to be specific about what you mean, biological
redundancy or sequence redundancy? I know refseq tries to specifically remove
biological redundancy (collecting together duplicate copies of the same genes). The
sequence redundancy is removed in uniprot in the uniparc sequence database.

Also SwissProt keeps spice variant information implicit in comment lines which you
can parse to get the variant sequences (this is what they do in uniparc).

How does Refseq deal with splice variants / sequence redundancy?

Has anyone done large scale comparison of the two databases?

Cheers,
Dan.


++ Stefanie Lager--
> It's redundancy both in Uniprot and In Refseq. Refseq contain splice
> variants but no fragments, it has good coverage. While SwissProt doesn't
> contain fragments or spice variants, but the coverage isn't quite as
> good. But TrEMBL does contain fragments and  splice variants. For a few
> species the IPI database could be an alternative
> http://www.ebi.ac.uk/IPI/IPIhelp.html  . It's a mergeer of UniProt,
> RefSeq and Ensembl. IPI has good coverage, and it contains splice
> variants, but few fragments.
>
> Stefanie
>
>> Hi, all,
>>
>> Recently,  I am working on the protein sequence analysis.  I found the
>> Refseq is very different from Uniprot.  Uniprot contains much more
>> proteins if TrEMBL is included.  Can any experts give some comments on
>> these two protein database.  Which one is more reliable?   It seems
>> Swiss is of the best quality, then Refseq, then TrEMBL.   And also, It
>> seems there are redundancy in Uniprot.  Is that so?
>>
>> -Frank
>>
>>
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