Questions tagged [uniprot]

The tag has no usage guidance.

Filter by
Sorted by
Tagged with
0
votes
2answers
36 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
vote
1answer
50 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 ...
2
votes
1answer
61 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
votes
1answer
123 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 ...
0
votes
1answer
35 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
votes
1answer
27 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
votes
1answer
108 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 ...
-2
votes
2answers
168 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
votes
2answers
66 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
votes
2answers
107 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 ...
3
votes
0answers
105 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
votes
2answers
279 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
votes
0answers
303 views

Converting XLOC ids to UNIPROT ids

A friend of mine has sent me an Excel file with the results of the cuff-diff program that has the following header: ...
0
votes
2answers
135 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 ...