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Questions tagged [uniprot]

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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
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2 votes
0 answers
16 views

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
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
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
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1 vote
0 answers
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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
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
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
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
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
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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