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4 votes

How to interpret UniProt allele patterns?

These are cytotoxic T-cell HLA alleles. HLA genotyping is very common and easy to do, so Genbank is the repository. A*11:01 has very high frequency in Aborigine populations here . You can explore the ...
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  • 6,967
4 votes

How to access organism IDS, taxon nodes from UniProt?

These are NCBI taxonomy ID's rather than anything specific to UniProt. One way to parse them would be using BioPython via Bio.Entrez, for example: ...
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4 votes
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How to retrieve the yeast locus tag from uniprot via sparql?

Ok, figured it out by looking at the scheme uniprot provides: ...
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  • 743
4 votes

How to get all PDB homologs from Uniprot (mapping + BLAST)?

For the correspondence between PDB and Uniprot entries you can use SIFTS -- a semi-automated mapping between PDB and UniProt maintained by PDBe. The pipeline that creates the mappings uses BLAST and ...
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  • 1,036
4 votes
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How do I get GO annotations for a list of UniProt IDs?

The link to the FTP for the GOA database files is listed on the GOA Downloads page. The file containing the mapping info you seek, goa_uniprot.all, comes in two ...
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4 votes

Is there a publication database or search engine offering geneID or UniProtID correlation?

I think this could be close to what you're looking for: http://glad4u.zhang-lab.org/index.php Paper: GLAD4U: deriving and prioritizing gene lists from PubMed literature It works with gene names though,...
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3 votes
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Why is the UniProt REST API returning multiple results, when I am only providing one ID to be checked?

it is because you do a text search and the "word" Q9UJL9 appears in multiple entries. If you want an id search, specifically say so and for that the query syntax is ...
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  • 146
2 votes

Cross-reference with PDB database

You can use the SIFTS mapping: http://www.ebi.ac.uk/pdbe/docs/sifts/ From an article: The Structure Integration with Function, Taxonomy and Sequences resource (SIFTS; http://pdbe.org/sifts) is a ...
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  • 1,036
2 votes

Cross-reference with PDB database

The UniProt website offers an ID mapping tool that tends to work pretty well: Then, hit "submit" and you will get the list of corresponding PDB IDs:
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  • 7,957
2 votes

Is there a tool that can take a protein's amino acid sequence and would display it's locus on the genome?

I think the mistake here is thinking that you need to use the sequence in order to find the genome co-ordinates. If these proteins come from a well annotated speices, you can easily do this with ...
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  • 3,201
2 votes

In Uniprot how do I know which variants are mutations and which are polymorphic?

This answer is very late but may still help others: Have a look at the UniProt index of human polymorphisms and disease mutations at https://www.uniprot.org/docs/humsavar Please don't hesitate to ...
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2 votes
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Loading all PPI information from Uniprot into a graph in NetworkX

The query link for all interactors would be thus : https://www.uniprot.org/uniprot/?query=organism%3A9606+AND+interactor%3A*&sort=score There is always an ...
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  • 270
2 votes

How to retrieve the subcellular location info from uniprot?

Since you are already on UniProtKB, the simplest way will be if you add this information to the output table and download it as a that you can import and filter in R. To get additional annotations, ...
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  • 788
2 votes

How to get Uniprot and swissprot cross references using Biopython

I believe the attribute you should be looking for is dbxrefs: [x for x in record.dbxrefs if x.startswith('GO:')] Apparently <...
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2 votes
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How to programmatically classify a protein according to its genbank feature

Using the UniProt website API (https://www.uniprot.org/help/api) this could be done with a query like https://www.uniprot.org/uniprot/?query=name%3A%22type%20IV%20secretion%20protein%20Rhs%22&...
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2 votes

Organelle genome genes

You can use the UniProt Advanced search for this. If you look at this help page https://www.uniprot.org/help/advanced_search, in particular the first example screenshot, you can type "encoded&...
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2 votes
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Efficient way of mapping UniProt IDs to representative UniRef90 IDs?

You can do this directly on UniProt: https://www.uniprot.org/uploadlists/ Just paste or upload your list of UniProt IDs, and select "UniProtKB AC/ID" in the "From" field and "...
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2 votes
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Where can we download a curated dataframe of the full archive of UniProt?

Answer from @matteo-ferla, converted from comment: There are many tables in the downloads page such tables enumerating each protein in a species proteome with basic stats, but not all the data. The ...
1 vote

Is there a publication database or search engine offering geneID or UniProtID correlation?

Take a look at GeneWalk, https://churchman.med.harvard.edu/genewalk. It's a very interesting solution to this rather difficult problem. It is well documented and packaged. But It's open source ...
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1 vote

It is possible to have a UniProt protein entry that does not have any genomic coordinates, because lacks of an Ensembl link?

If you look at this query https://www.uniprot.org/uniprot/?query=NOT%20database:(type:ensembl)&fil=organism:%22Homo%20sapiens%20(Human)%20[9606]%22&sort=score and restrict it to the reference ...
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1 vote

How to extract all peptide sequences for a UniProt protein entry with an API?

If downloading the complete database is not an option, you may able to use the instructions from this help page (based on the gff format for any given query): https://www.uniprot.org/help/...
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1 vote

how could i find uniprot ac in blast?

UniProt also provides a BLAST service (https://www.uniprot.org/blast), or you could use the Expasy BLAST too, at https://web.expasy.org/blast. If you have performed your similarity search at NCBI or ...
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1 vote
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Infer the new (Ban et. al) ribosomal nomenlature (ex. uL53 ) from the ribosomal protein's sequence

This is a copy-paste nearly verbatim of comments so that the question has an answer What you are trying to do is find what genes are in what homology cluster. This is common problem and there are ...
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1 vote
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How can I find all the columns available in UniProt.ws package for R?

From the UniProt.ws manual: columns shows which kinds of data can be returned for the ...
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  • 3,462
1 vote

How can I find all the columns available in UniProt.ws package for R?

Do you have a small sample of the proteins you are looking for and what you have tried so far in R using Uniprot.ws ? (including output of it), it could be helpful to identify your problem and how to ...
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  • 1,021
1 vote
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UniProt flat file. Interpreting format of SUBCELLULAR LOCATION. What does flag mean?

Thank you for asking this question. "Flag" is actually an obsolete notation which predates the introduction of proper evidence attribution in UniProtKB, and which escaped us in our efforts to update ...
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1 vote

Web scraping in R

I don't have a complete answer to your question, but as a primer I can tell you that you should look into the Bioconductor packages. The reason is that biological sequence data are deposited in online ...
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  • 111
1 vote

Web scraping in R

You can search databases like Cosmic(Cancer) with the gene names to get frequently occurring mutations in cancer. I'm not sure about any specific tool/pipeline available for this exact scenario. As ...
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  • 584
1 vote

Is there a tool that can take a protein's amino acid sequence and would display it's locus on the genome?

Have you tried BLAST, or specifically tBLASTn? This will take a protein and compare it any set of reference genomes. You can also BLAST multiple sequences at once.
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1 vote

How to get all PDB homologs from Uniprot (mapping + BLAST)?

You can download a BLAST db containing all sequences of proteins in Uniprot and in the PDB. The way I would go about this is first download the databases for uniprot and PDB, then query the PDB ...
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