Hi,
I just ran into a problem regarding isoforms specified in Uniprot XML files which are not present in the 'every' isoform fasta file available in Uniprot.
One example would be the protein: Q8IYH5 where we can find the following isoforms:
<comment type="alternative products">
<event type="alternative splicing"/>
<isoform>
<id>Q8IYH5-1</id>
<name>1</name>
<sequence type="displayed"/>
</isoform>
<isoform>
<id>Q8IYH5-2</id>
<name>2</name>
<sequence type="described" ref="VSP_025511"/>
</isoform>
<isoform>
<id>Q8IYH5-3</id>
<name>3</name>
<sequence type="described" ref="VSP_025509 VSP_025510"/>
<note>No experimental confirmation available.</note>
</isoform>
<isoform>
<id>Q8IYH5-4</id>
<name>4</name>
<sequence type="described" ref="VSP_025512 VSP_025513"/>
<note>No experimental confirmation available.</note>
</isoform>
</comment>
Most of them can be found in the general isoform fasta file, however the isoform with ID: Q8IYH5-1 is not present in the file.
Do you know if this is a bug/isolated case? Is there any reason/relationship between the ones missing here?
Thanks in advance,
Pablo
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Pablo Pareja
Sorry, this is my first post - I just posted my reply as a comment by mistake.
Here you go again:
The isoform fasta file (uniprot_sprot_varsplic.fasta) only contains additional isoforms (see ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/README.varsplic) and not the "canonical" sequences, i.e. those marked
<sequence type="displayed"/>
in the xml.
The isoform file needs to be combined with the file uniprot_sprot.dat (or uniprot_sprot.fasta) to obtain all isoform sequences.
See also
What is the canonical sequence? http://www.uniprot.org/faq/30
How to retrieve sets of protein sequences? http://www.uniprot.org/faq/38
Elisabeth
Thanks for your quick answer, I have a few remarks about this though. Why not including information about the isoform like name and sequence in the XML files? Besides that, I just downloaded the file uniprot_sprot.fasta and there is no entry for the isoform Q8IYH5-1 here either. Should it be somewhere else?
Isoform names are in the xml: see e.g. <name>1</name> in your above example.
Sequences are not, I can check for you whether this has ever been discussed.
Q8IYH5-1 is the displayed (canonical) sequence of Q8IYH5, and its sequence is therefore identical to that of Q8IYH5. uniprot_sprot.fasta has an entry for all canonical isoforms, including Q8IYH5.
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Hi Pablo, the isoform fasta file (uniprotsprotvarsplic.fasta) only contains additional isoforms (see ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/README.varsplic) and not the "canonical" sequences, i.e. those marked <sequence type="displayed"/>
The isoform file needs to be combined with the file uniprotsprot.dat (or uniprotsprot.fasta) to obtain all isoform sequences.
See also What is the canonical sequence? http://www.uniprot.org/faq/30 How to retrieve sets of protein sequences? http://www.uniprot.org/faq/38
Elisabeth