Questions tagged [uniprot]

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

I have a list of UniProt codes and I am trying to fetch the genomic coordinates through the API from programmatic access to UniProtKB (https://www.ebi.ac.uk/proteins/api/doc/). Moreover, I read that ...
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18 views

Best resource to link a gene/protein to a druggability score?

Could I ask, is anyone familiar with the Drugebility score provided by Chembl? I wanted to add a druggability score to a set of human targets, to understand the likelihood that they are druggable. I ...
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Why is there a drop in the publication's rate of protein-sequences in UniProtKB/SwissProt

UniProt provides two databases 1: UniProtKB/TrEMBL (TE) with entries for which the annotations are derived from the European Nucleotide Archive. UniProtKB/SwissProt (SP) with entries for which the ...
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1answer
46 views

How do I get GO annotations for a list of UniProt IDs?

I have a list of UniProt ids that I want to get Gene Ontology annotations for. I need this information because I want this high-level information as an input to a neural network. The model I wish to ...
2
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1answer
37 views

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

I know how to generally pull down information for a UniProt entry using the REST API, for example: https://www.uniprot.org/uniprot/?query=id:Q9UJL9&sort=score&columns=id,go(molecular%...
2
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1answer
29 views

Why is the UniProt REST API returning multiple results, when I am only providing one ID to be checked?

Can some explain why when I run a REST API query on UniProt for one ID ('Q9UJL9'), the results for three IDs are returned? The query I'm using is: https://www.uniprot.org/uniprot/?query=Q9UJL9&...
2
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1answer
61 views

How to programmatically classify a protein according to its genbank feature

Say I found an interesting protein in a genbank file, e.g.: ...
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0answers
47 views

How to deal with the mismatches between gene names obtained from different sources?

For most of the time, I rely on gene ids to combine different datasets. However, in some instances, I have to combine datasets based on gene names. Then, if I don't know the source of gene names in ...
1
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1answer
55 views

How to get the uniparc ids for all members of uniref cluster in batch request?

I currently use the 'UniProt website REST API' (example) to collect the UniParc IDs of all the members of the given cluster. Fetching each entry individually is very slow though, so I wanted to ask if ...
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1answer
28 views

how could i find uniprot ac in blast?

I have made a search in p-blast. I would like to search for the protein results in uniprot. how can I do it directly? I can go to GENBANK but i would like to go to UNIPROT. Thank you!!!
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2answers
28 views

how can i search in p-blast against UNIPROT(not only swissprot)

i need to search for one protein against UNIPROT in BLAST for a selected organism. How can I do it? (SWSISSPROT+TREMBL) THANKS!!
1
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1answer
67 views

Loading all PPI information from Uniprot into a graph in NetworkX

I am looking for guidance to load all SwissProt PPI data for Homo sapiens into a graph (from NetworkX). In particular, the part that I'm struggling with is gathering the data from SwissProt for each ...
2
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0answers
36 views

Get nucleic acids' chain names from PDB API

There is a place in my pipeline where I call PDB's API with a ribosomal id to get all the subchains of that molecule programmatically I'd like to separate subchains that are proteins from nucleic ...
2
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1answer
86 views

Infer the new (Ban et. al) ribosomal nomenlature (ex. uL53 ) from the ribosomal protein's sequence

I'm trying to programmatically construct a name for each protein subchain in any ribosome from Uniprot in accordance with Ban et. al's 2014 proposal (excerpt given below) using PDB's and Uniprot's ...
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2answers
172 views

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

I am trying to find the subcellular localization of my 10,000 proteins using UniProt.ws package for R. However, I am unable to find all the columns available for query. I used another package named ...
1
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2answers
462 views

How to retrieve the subcellular location info from uniprot?

I have a list of proteins with their gene names/symbols. I would like to identify which of them are extracellular proteins or plasma membrane proteins. I can get this information in UniprotKB by ...
1
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1answer
154 views

How to get Uniprot and swissprot cross references using Biopython

I am struggling to use biopython to gather cross references such as GO annotation from Uniprot/swissprot text files ("DR" in the .txt files) using biopython. From ...
3
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1answer
80 views

How to interpret UniProt allele patterns?

In creating a parser for the UniProt flat file uniprot_sprot.dat (directory) in the manual for the comments POLYMORPHISM there ...
2
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1answer
161 views

UniProt flat file. Interpreting format of SUBCELLULAR LOCATION. What does flag mean?

In creating a parser for the UniProt flat file uniprot_sprot.dat (directory) in the manual for the section SUBCELLULAR LOCATION ...
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1answer
37 views

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

In Uniprot how do I know which variants are mutations and which are polymorphic? I am looking at P38398 (BRCA1_HUMAN) specifically. Many thanks.
2
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1answer
35 views

How to get all chemical compounds that interact with a given protein target?

I want to get all Pubchem Chemical compounds (CID) that interact with a given UniProt target. I have a list of UniProt targets and I need to study the relationship between these targets and chemical ...
3
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1answer
123 views

How to retrieve the yeast locus tag from uniprot via sparql?

Let's say I want to retrieve the yeast-specific identifier for a certain protein, in the example below it will be P00330 which I would like to link to YOL086C. When I go to uniprot's sparql UI and ...
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2answers
277 views

Web scraping in R

I have ~130 gene names of different human proteins. I'm looking for a convenient and systematic way to locate each gene's location in the genome, extract its CDS sequence and find whether there are ...
3
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2answers
102 views

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

I have the UNIPROT IDs, PDB IDs and FASTA files of several known proteins. I am looking for a tool that can take as input the protein's amino acid sequence and display the coding nucleotides of those ...
4
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2answers
137 views

Cross-reference with PDB database

I have a list of several thousand proteins and their UNIPROT IDs. I'm looking for an efficient method of cross-referencing it against the PDB tertiary structure database, and get a list of those ...
4
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0answers
210 views

Map domain names from UniProt bed files to domain accessions

I want to get a bed file mapping human protein domains to the human genome. UniProt actually offers such a thing here. The problem, however, is that the file doesn't include any kind of domain ...
7
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2answers
480 views

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

I'd like to create a dataset consisting of all sequences which are either present in the PDB, or whose homolog is present in the PDB. In other words, any sequence in the PDB or any sequence related to ...
0
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2answers
156 views

How to access organism IDS, taxon nodes from UniProt?

I try to find organism IDs used by UniProt (e.g. 9606 for "Homo sapiens") and information about the 'taxonomic kingdom' this organism belongs to. The only source on UniProt I could find is this file ...