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Confusion with queries on UniProt

New to the UniProt API and RestAPIs in general, so I'm really confused why 3 seemingly identical queries yield a different number of results. 1: https://www.uniprot.org/uniref/UniRef90_P01009 yields ...
Jason Liang's user avatar
1 vote
0 answers
14 views

Discrepancy between UniProt and AlphaFold data for MlaD domains – Seeking guidance on automating entry sorting based on accurate domain count

Hey fellow researchers, I recently conducted an analysis on the UniProt database, specifically focusing on entries with MlaD domains. After downloading the data and opening it in an Excel file, I ...
Deepankar's user avatar
0 votes
1 answer
49 views

Fetching Protein Sequences through UniPROT gives ConnectionError

I have 193000 protein interactions in CSV named all_proteininteractions.csv which have query protein name in the 2nd column and partner protein in the 3rd like this:...
Anas Jamshed's user avatar
0 votes
1 answer
57 views

Fetching uniprot seq using bash command

I am trying to get a protein sequence using this command: curl https://www.uniprot.org/uniprot/A2Z669.fasta But I don't get any output: ...
Younes Abuelayyan's user avatar
0 votes
2 answers
73 views

How long should it take to cluster Uniref?

I have the Uniref90 dataset containing around 76M sequences. I have made modifications to all sequences based on a reduced amino acid alphabet. I am trying to cluster it again at 90% identity. I am ...
GIONII's user avatar
  • 11
1 vote
0 answers
43 views

Where/How can I download all proteins in the UniProt with signal peptide annotated?

Where/How can I download all proteins in the UniProt with signal peptide annotated? I downloaded the uniref50.xml. However, the annotation information is not contained. In an XML record of a protein, ...
jinyuan sun's user avatar
2 votes
1 answer
35 views

Retrieval protein definition from accession ID

I have a list of protein accessions: XP_025107904.1 PVD22034.1 AJA37836.1 How can I obtain the definition of the protein, and the related organism? Output: ...
Marco's user avatar
  • 161
2 votes
2 answers
208 views

Get genome coordinates from UniProt entry?

I'm trying to get genome coordinate information programmatically for multiple genes. As an example, I'd like to get the annotation (list of exons and their chromosomes, starts, and ends) for this ...
Michael Dunne's user avatar
2 votes
1 answer
66 views

Mapping PDB ID + chain ID to UniProt ID

This question was addressed here. Unfortunately, including bioservices, the solutions pypdb and ...
Johnny Tam's user avatar
1 vote
0 answers
110 views

How to annotate list of proteins with KEGG orthology groups?

I've got a list of proteins, complete with Uniprot IDs (for some of them) and gene names. I'd like to group them into orthology groups based on data from KEGG, but I have no idea how to add a column ...
Empiromancer's user avatar
2 votes
0 answers
18 views

Active sites of the query protein does not align with the top hit using HHpred

I am having difficulties with an alignment on HHpred and was wondering if anyone had any answer to the following: I am trying to align my protein (PDB 2VU9, a Botulinum Neurotoxin Type a) with one of ...
microbeprincess's user avatar
2 votes
1 answer
261 views

Efficient way of mapping UniProt IDs to representative UniRef90 IDs?

I want to map ~500,000 UniProt IDs to their representative UniRef90 IDs. What is the most efficient way of doing this? Do we have a table with the mapping?
Johnny Tam's user avatar
3 votes
1 answer
41 views

Where can we download a curated dataframe of the full archive of UniProt?

I want to download a curated dataframe of the full archive of UniProt. Any format as long as it is a table (.csv, .tsv, ...
Johnny Tam's user avatar
3 votes
1 answer
151 views

Relationship between entries for same UniProt Id

I was playing around, looking at some AlphaFold predictions for certain proteins and I realized that sometimes the sequences of aminoacid look very different for the same UniProt id. For example, 15C8 ...
CubeHead's user avatar
  • 425
2 votes
2 answers
47 views

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

Do we have a publication database or search engine that offers geneID or UniProtID correlation? For example, I search "IPS cells" -> I want to know what genes or proteins are under active ...
Johnny Tam's user avatar
2 votes
1 answer
34 views

Organelle genome genes

How can I get all proteins coded by mitochondrial genome or plastid genome from UniProt. I see UniProt has multiple filtering and search parameters but I could not distinguish between proteins/genes ...
abelfit's user avatar
  • 73
2 votes
1 answer
44 views

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 ...
Giamma Fer's user avatar
0 votes
0 answers
75 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 ...
Slowat_Kela's user avatar
4 votes
1 answer
774 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 ...
ChemBot's user avatar
  • 43
2 votes
1 answer
245 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%...
Slowat_Kela's user avatar
2 votes
1 answer
85 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&...
Slowat_Kela's user avatar
2 votes
1 answer
71 views

How to programmatically classify a protein according to its genbank feature

Say I found an interesting protein in a genbank file, e.g.: ...
Oren Milman's user avatar
1 vote
0 answers
154 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 ...
user345394's user avatar
3 votes
1 answer
379 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 ...
C. Zeil's user avatar
  • 121
0 votes
1 answer
49 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!!!
marilu's user avatar
  • 101
0 votes
2 answers
163 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!!
marilu's user avatar
  • 101
1 vote
1 answer
152 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 ...
An Ignorant Wanderer's user avatar
2 votes
0 answers
73 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 ...
rtviii's user avatar
  • 364
2 votes
1 answer
94 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 ...
rtviii's user avatar
  • 364
1 vote
2 answers
362 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 ...
Riq's user avatar
  • 35
1 vote
2 answers
1k 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 ...
Jun's user avatar
  • 11
2 votes
1 answer
272 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 ...
James's user avatar
  • 409
3 votes
1 answer
95 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 ...
Guy Coder's user avatar
  • 315
2 votes
1 answer
213 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 ...
Guy Coder's user avatar
  • 315
0 votes
1 answer
42 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.
Antonio's user avatar
2 votes
1 answer
50 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 ...
Eman Ismail's user avatar
3 votes
1 answer
153 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 ...
Cleb's user avatar
  • 743
-1 votes
2 answers
375 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 ...
Adrian Smith's user avatar
3 votes
2 answers
215 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 ...
Adrian Smith's user avatar
4 votes
2 answers
178 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 ...
Adrian Smith's user avatar
5 votes
0 answers
285 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 ...
terdon's user avatar
  • 10.2k
7 votes
2 answers
649 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 ...
Zubo's user avatar
  • 179
0 votes
2 answers
213 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 ...
Cleb's user avatar
  • 743