[BiO BB] difference between Refseq and Uniprot
lifei03 at gmail.com
Mon Jun 27 07:09:08 EDT 2005
From the gpff.gz file in Refseq database, transcrpit varaiants of genes
are given as independant items. I am giving an example of transcrpits
annotation in RefSeq database here
LOCUS NP_739577 433 aa linear PRI
Transcript Variant: This variant (2) lacks an in-frame segment of
the coding region, compared to variant 1. It encodes a shorter
isoform (2), that is missing an internal segment compared to
Dan Bolser wrote:
>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?
>++ 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.
>>>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?
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