Details
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Type:
Improvement
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Status: Ready for testing
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Priority:
Minor
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Resolution: Unresolved
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Affects Version/s: 2.11.4.0
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Fix Version/s: None
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Component/s: data retrieval services
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Labels:None
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Environment:MacOS Seqouia (15.0)
Description
I've just been running through an (inherited) UG workshop I'm running next week, which involves students using NCBI blast to identify similar proteins from UniProtKB, then retrieving those sequences into Jalview to carry out a MSA.
This simple workflow fails since NCBI blast reports UniProt accessions including a sequence version (i.e. P23953.4). Using these accessions as they stand in the sequence fetcher fails, since a 'true' uniprot accession is not versioned - these come from UniParc. Stripping the version off successfully retrieves the sequences.
Arguably the current behaviour is correct - UniProtKB does not include an SV in it's accession, so these are not valid accessions, however the behaviour is counterintuitive and non-obvious to the less experienced who are not familiar with sequence versions. Since this is how NCBI BLAST is returning the accessions though, it would make sense to strip off the sequence version to ease moving between different resources.
This simple workflow fails since NCBI blast reports UniProt accessions including a sequence version (i.e. P23953.4). Using these accessions as they stand in the sequence fetcher fails, since a 'true' uniprot accession is not versioned - these come from UniParc. Stripping the version off successfully retrieves the sequences.
Arguably the current behaviour is correct - UniProtKB does not include an SV in it's accession, so these are not valid accessions, however the behaviour is counterintuitive and non-obvious to the less experienced who are not familiar with sequence versions. Since this is how NCBI BLAST is returning the accessions though, it would make sense to strip off the sequence version to ease moving between different resources.
