User: me

gravatar for me
me690
Reputation:
690
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Trusted
Location:
Switzerland
Twitter:
@jervenbolleman
Last seen:
1 month ago
Joined:
4 years, 10 months ago
Email:
m*@jerven.eu

Posts by me

<prev • 64 results • page 1 of 7 • next >
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Comment: C: convert protein accession number to description
... Could you describe what exactly you mean by "description" ...
written 4 weeks ago by me690
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Comment: C: convert protein accession number to description
... This will fail in a large number of cases as the NCBI does not have all UniProt accessions. ...
written 4 weeks ago by me690
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Comment: C: How to download the .dat file of the UniProt Metazoa?
... The UniProt flat file format is not the same as the EMBL format even if it is quite close. So you might run into issues if your software expects real EMBL. ...
written 5 weeks ago by me690
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Comment: C: Extracting Sub-cellular location from Uniprot into tabular format
... We are at SIB Swiss-Prot working on UniProt are offsite, wait until thursday ;) ...
written 7 months ago by me690
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Comment: C: How to retrieve EC numbers and KOs for proteins of several taxons?
... By chemistry is a bit limited so I need my colleague to help with stoichiometric factors and it's production week so time is hard to get. ...
written 8 months ago by me690
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Comment: C: How to retrieve EC numbers and KOs for proteins of several taxons?
... Running out of space for the Rhea part, we will make a separate Q&A ...
written 8 months ago by me690
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Answer: A: How to retrieve EC numbers and KOs for proteins of several taxons?
... 1) Is correct in the query with ?protein up:reviewed true . 2) The query in the Q. does not return anything for taxon:3702 as there are no rdfs:subClasses for Aribidopsis Thaliana, it is a leaf node. This means the entry is directly linked to that taxon instead of via it's ancestors. This i ...
written 8 months ago by me690
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Comment: C: Importing Uniprot into BioSQL using BioPython takes years (nearly literally!)
... It would probably work ok on our endpoint. But I think we got just the tool [you want, namely prosite][1]. I would also have a look at not using a database at all in that case as they will not perform optimally for your use case. [1]: https://prosite.expasy.org/scanprosite/ ...
written 12 months ago by me690
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Comment: C: Importing Uniprot into BioSQL using BioPython takes years (nearly literally!)
... This is a comment because it is not at all answering your question. Instead of building your own database why not use our SPARQL.uniprot.org. This is likely to be better modelled than biosql is for the UniProt datamodel. Otherwise I suspect your hardware is not at the level that one would use for ...
written 12 months ago by me690
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Answer: A: UniProt SPARQL: retrieving proteins of a complete proteome (Escherichia coli K12
... There are two issues with this query. The first is that in the PREFIX declaration there is an s missing at the end of proteome i.e. PREFIX proteome: should be PREFIX proteome: The second one is more frustrating and is that the character '#' used in the fragment IRI is also seen as the ...
written 12 months ago by me690

Latest awards to me

Voter 6 months ago, voted more than 100 times.
Scholar 8 months ago, created an answer that has been accepted. For A: Does UniProt have complete SNP information (from dbSNP)?
Popular Question 8 months ago, created a question with more than 1,000 views. For Image analysis specialist / scientific programmer | sciCORE University of Basel
Popular Question 12 months ago, created a question with more than 1,000 views. For Image analysis specialist / scientific programmer | sciCORE University of Basel
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: Downloading dataset of PTM sites from UniProt
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Scholar 15 months ago, created an answer that has been accepted. For A: Does UniProt have complete SNP information (from dbSNP)?
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Get MW of a protein given a uniprot ID in R
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Get MW of a protein given a uniprot ID in R
Commentator 2.0 years ago, created a comment with at least 3 up-votes. For C: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Scholar 2.3 years ago, created an answer that has been accepted. For A: Get MW of a protein given a uniprot ID in R
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Get MW of a protein given a uniprot ID in R
Supporter 2.3 years ago, voted at least 25 times.
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Get MW of a protein given a uniprot ID in R
Commentator 4.2 years ago, created a comment with at least 3 up-votes. For C: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Teacher 4.3 years ago, created an answer with at least 3 up-votes. For A: Get MW of a protein given a uniprot ID in R
Scholar 4.3 years ago, created an answer that has been accepted. For A: Get MW of a protein given a uniprot ID in R
Scholar 4.4 years ago, created an answer that has been accepted. For A: Get MW of a protein given a uniprot ID in R
Scholar 4.5 years ago, created an answer that has been accepted. For A: Get MW of a protein given a uniprot ID in R
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: Get MW of a protein given a uniprot ID in R

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