User: me

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me680
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680
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@jervenbolleman
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1 month ago
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4 years, 5 months ago
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m*@jerven.eu

Posts by me

<prev • 61 results • page 1 of 7 • next >
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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 12 weeks ago by me680
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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 3 months ago by me680
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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 3 months ago by me680
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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 3 months ago by me680
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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 7 months ago by me680
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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 7 months ago by me680
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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 7 months ago by me680
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Comment: C: Substring dereplication of protein sequences
... [pir peptide search][1] could be helpful even if it does not answer your question. [1]: https://research.bioinformatics.udel.edu/peptidematch/commandlinetool.jsp ...
written 9 months ago by me680
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Comment: C: UniProt ID mapping API call
... Well they would be in a significant part be me ;) You can use the upload list facility on www.uniprot.org as well. Then you can use what ever columns you want. The real difficulty is actually with gene names and how they map to/from UniProt entries. The solutions to that are ask for exactly what you ...
written 10 months ago by me680
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Comment: C: UniProt ID mapping API call
... if you want the species/ncbi taxid just add a line "?protein up:organism ?taxon ." at the end of the where clause and "?taxon" on the select line. ...
written 10 months ago by me680

Latest awards to me

Scholar 3 months ago, created an answer that has been accepted. For A: Does UniProt have complete SNP information (from dbSNP)?
Popular Question 3 months ago, created a question with more than 1,000 views. For Image analysis specialist / scientific programmer | sciCORE University of Basel
Popular Question 6 months ago, created a question with more than 1,000 views. For Image analysis specialist / scientific programmer | sciCORE University of Basel
Teacher 7 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 9 months ago, created an answer that was upvoted at least 5 times. For A: Downloading dataset of PTM sites from UniProt
Teacher 9 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 10 months ago, created an answer that has been accepted. For A: Does UniProt have complete SNP information (from dbSNP)?
Teacher 10 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 11 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 11 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 15 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 19 months 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 22 months ago, created an answer that has been accepted. For A: Get MW of a protein given a uniprot ID in R
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Teacher 23 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 3.8 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 3.8 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 3.8 years ago, created an answer that has been accepted. For A: Get MW of a protein given a uniprot ID in R
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Teacher 4.1 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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