Questions tagged [public-databases]
Use this tag for questions about how to use, download, retrieve, check and browse public databases.
116
questions
1
vote
1
answer
28
views
PANTHER FUNCTIONAL CLASSIFICATION in R
Does anyone know of a way to programmatically get panther protein class terms and IDs for a gene list, in a way that the classification structure is preserved (PARENT CLASS + CHILD CLASS)?
i.e. For a ...
- 11
0
votes
0
answers
8
views
Exporting Panther functional classification of gene list
After inputting a list of gene and running an analysis in https://www.pantherdb.org/ (such as "functional classification"), I get a result table that is limited by an X number of entries ...
- 21
1
vote
0
answers
30
views
1
vote
1
answer
20
views
What happened to the PhyLoTA browser?
A paper I'm reading from 2021[1] mentions doing some analysis on data from the PhyLoTA database, with this reference citation:
M. J. Sanderson et. al. 2008 The PhyLoTa Browser: processing GenBank for ...
M__♦
- 11.9k
5
votes
2
answers
171
views
Converting VCF format to text for use with PLINK and understanding column mapping
I successfully completed Nature PRS tutorial, which is based on PLINK. Turning to my real data, I downloaded ukb-d-20544_1.vcf.gz. Now I'm facing the problem that I seem to be unable to use it in ...
- 513
3
votes
1
answer
117
views
What tools can I use to look up my alleles, genotypes, or phenotypes from my sequenced DNA (WGS)?
I bought a "Whole Genome Sequence" kit, which gave me the following VCF files (this service did not include any analysis, just the raw data):
cnv.vcf
<...
- 1,679
8
votes
2
answers
11k
views
Converting Ensembl Gene IDs to Entrez Gene IDs through biomart
Well, I'm trying to convert a list of Human Gene referenced by Ensembl Gene IDs to Entrez Gene IDs. I have been advised to use biomart.
I tried to get a kind of conversion table for all human genes. ...
- 335
4
votes
1
answer
69
views
Where can I find lncRNA expression data for different cell types?
Are there any publicly available databases singularly providing expression data for any given long non-coding RNA (lncRNA) for
varying cell types
any species
preferably including humans?
...
CommunityBot
- 1
4
votes
1
answer
221
views
How to get a GISAID account? I registered months ago, still no reply!
Inspired by amateur variant hunters, I would like to join the Pango lineage proposal community and help contribute to variant surveillance.
However, I cannot seem to get access to GISAID, the platform ...
M__♦
- 11.9k
2
votes
1
answer
34
views
NCBI Blast databases - cannot find some databases
I'm working with a system that does local BLAST searches using some preconfigured BLAST databases. From what I see, these were updated within the last year, but I cannot find any current databases ...
M__♦
- 11.9k
1
vote
2
answers
104
views
How many protein sequences do we usually have for each species?
My question is exactly the one in the title. I add a particular example for more clarity. If I want to study the sequence of protein IkBα, do I find only one sequence or is there a database that ...
M__♦
- 11.9k
1
vote
1
answer
63
views
Gene rank scores from LINCS database: Evangelista et al. 2022
The website https://maayanlab.cloud/sigcom-lincs/#/SignatureSearch/UpDown can be used to "Identify reversers and mimickers from over 1 million signatures by entering up and down gene sets .. &...
M__♦
- 11.9k
0
votes
0
answers
31
views
Get BioProject code of a GEO dataset
In publications the GEO code is usually shared and not the BioProject/study code.
I want to get the BioProject/Study Accession code of a GEO dataset (to later download the data from ENA).
I know that ...
- 13.8k
10
votes
2
answers
1k
views
Is there a database of disease prevalence?
I want to collect data on how common different diseases are in different populations (or, at least, globally). Ideally, it would give me a way of querying the database with a disease name, and would ...
- 9,662
1
vote
1
answer
49
views
Transcript vs Primary transcript on phytozome
Could someone help me understand what the difference between transcript and primary transcript on phytozme is? For example, this dataset of A.thaliana has "primary transcript CDS" vs CDS.
...
- 217
2
votes
1
answer
58
views
Get a comprehensive list of virulence factors for certain or all pathogens?
Is there a database with all known proteins/genes of specific pathogens such as Staph aureus and annotated whether it is a known virulence or resistance factor that idealy can be downloaded in table ...
- 3,804
2
votes
1
answer
320
views
how to download all metadata for a single TCGA dataset and link to data file UUIDs?
I've been able to download specific data types from the TCGA portal (https://portal.gdc.cancer.gov/) using the Manifest files and the GDC Tool.
But it's not clear to me how to download the metadata (e....
- 1,295
1
vote
1
answer
48
views
Why do Illumina 850k/EPIC arrays ignore CpGs which are "GC" in the forward strand?
CpGs are symmetrical, in that a CG sequence on the forward strand is hybridized to a GC --- and both dinucleotides on each opposing strand are CpGs dinucleotides which can be methylated. Conversely, ...
- 141
1
vote
0
answers
130
views
Creating maps.fld file of protein for AutoDock GPU
I want to use AutoDock GPU, which accepts protein.maps.fld and ligand.pdbqt files.
Since I am performing high throughput virtual screening, shall I just load protein AutoDockTools and create protein....
M__♦
- 11.9k
5
votes
2
answers
381
views
How can I work out gram staining information from the species name?
I have a very long list of prokaryote organism names. I would like to know their gram staining (gram positive or gram negative) information.
Please let me know if there is any database that keeps ...
- 11
2
votes
0
answers
27
views
What data set was used Gene Expression Data of Postmortem Tissues?
I want to run the experiments "Sample Application to Genotype-Tissue Expression (GTEx) Project Gene Expression Data of Postmortem Tissues" mentioned in "Enter the Matrix: Factorization ...
- 487
1
vote
0
answers
46
views
GSEA. Subsetting Gene Ontology, Biological Processes, by gene set families of interest
I have run GSEA - on Gene Ontology , Biological Processes (GO and BP hereafter) - on some Mouse bulk RNA-seq data, and am currently in the process of going through the results. To do this, I have used ...
- 836
5
votes
1
answer
37
views
Are there any "canonical" sources of C. elegans connectome?
I found that there are a couple of projects that allow the user to simulate the neural system of C elegans, for example OpenWorm one update being here.
I don't know how to navigate sources in ...
CommunityBot
- 1
2
votes
4
answers
542
views
How can I obtain FTP links to studies in ENA given a BioProject ID?
How can I programmatically obtain ftp links to RNA seq fastq files in ENA? Here's an example of a link that I would be interested in obtaining:
...
- 527
5
votes
0
answers
267
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 ...
- 13.8k
1
vote
1
answer
6k
views
local BLAST error: BLAST Database error: Error: Not a valid version 4 database
I want to use a local blastn command to BLAST a multifasta file ~700 sequences using following command: ...
- 1
2
votes
0
answers
78
views
Mapping ICD9 codes in UKBB data to PheCodes using PheWAS package
I am working on the UKBB data and trying to specify cases and controls by converting ICD9 codes to PheCodes. I have input data (icdt) where the first column (f.eid) is patient IDs and the remaining ...
- 1,295
0
votes
4
answers
167
views
Where can I find Single Cell Data with Location "Coordinates"?
Does single cell data typically have the following meta-data: the "coordinates" (e.g. on a tissue, adjacent tissues) saying where each cell in the sample was located relative to other cells? ...
2
votes
0
answers
17
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 ...
M__♦
- 11.9k
1
vote
0
answers
52
views
Find the date that sequencing was performed
Background I've obtained RNAseq datasets from ENCODE and I'm looking to identify external variables contributing to sequence variance among these samples.
External variables For example, clustering ...
M__♦
- 11.9k
5
votes
0
answers
358
views
What exactly does each of InterPro, PANTHER, Pfam bring to the table individually in classifying a protein?
I would be very grateful if somebody could sketch out the methods Pfam and PANTHER use to assign a family to a given protein and how they are different. My (cursory) understanding is that InterpProp ...
M__♦
- 11.9k
2
votes
0
answers
294
views
Convert MeSH term to drugbank ID
I have set of annotated term of drugs extracted from PubTator those drugs are annotated in form of MeSH terms. I would like to map them into drugbank ID. I do search the the MeSH term i find the ...
M__♦
- 11.9k
1
vote
0
answers
24
views
Viral Load and Antiretroviral Therapy Dataset
My project is on Mathematical Modeling of the relationship between viral load and antiretroviral therapy. Its purely an academic investigation which is exploratory in nature.
Question I am seeking a ...
M__♦
- 11.9k
3
votes
2
answers
95
views
Retrieval of metadata of a batch of 3953 sequence data from GISAID database
I need to retrieve COVID-19 metadata (such as date of collection of sequence data, location, etc.) for a batch of 3953 GISAID accessions from the GISAID database.
I am not very comfortable with GISAID....
M__♦
- 11.9k
2
votes
0
answers
200
views
What is the difference between flat and stereo stitch id?
For my thesis, I'm working on side effect prediction in a machine learning framework and I am working on data available on SIDER (http://sideeffects.embl.de/download/). If you open the README file, ...
- 21
3
votes
2
answers
440
views
What happened to sra ftp server?
My whole (professional) life I am downloading sequences from SRA and ENA databases. Long time ago, I used prefetch from sra-tools, but later I switched to simply using wget from ftp servers of the two ...
- 13.8k
3
votes
0
answers
26
views
OMIM diseases to UMLS mapping
Is there any public available mapping between Online Mendelian Inheritance in Man (OMIM) diseases and Unified Medical Language System (UMLS) concepts?
OMIM has mapping for genes to entrez or ensembl, ...
- 5,517
3
votes
2
answers
131
views
How to get the number of complete phage genomes available on ncbi?
I am looking to establish the total number of complete phage genomes available on NCBI.
I am not looking for any specific type, but want to understand the total diversity available.
How can I perform ...
M__♦
- 11.9k
14
votes
3
answers
14k
views
How to obtain .bed file with coordinates of all genes
I want to get a .bed file with the genes' names and canonical coordinates, also I would like to have coordinates of exons, too. I can get the list from UCSC, however, if I choose UCSC Genes - ...
- 3,125
0
votes
1
answer
201
views
How to get a FASTA format file with the DNA sequences of all annotated genes?
I am analysing Pyrococcus Furiosus DNA sequencing data by considering data published here in NCBI. When I click on "Send to">"Gene Features">"FASTA format" I ...
2
votes
1
answer
381
views
dbSNP GRch37 Download
I am still new to this.
I am trying to download the GRch37 dbSNP data from the NCBI dbSNP Browser using the "Send to:" button. But whenever I select
"Send to:" > "File"...
- 2,086
1
vote
1
answer
202
views
Where to find publicly available Sanger chromatography data?
I am looking for any public available databases where I can download Sanger chromatography data ideally in Ab1 or SCF file format. I need extremely large amounts of this, since I want to use it for ...
- 151
0
votes
1
answer
28
views
Where can I find a basic example for testing association between a phenotype and each of the variants of a chromosome?
I am a statistics student trying to find data suitable for a particular method. From what I have read so far, it is of interest to determine if variants within a chromosome are associated with a ...
- 3,804
2
votes
1
answer
2k
views
How to download data from SRA in Linux systems via the command line?
My workflow for downloading data from SRA has been the following:
Access SRA Run Selector.
Enter the accession number for the project of interest.
Download "Accession List" for the "...
- 769
5
votes
0
answers
55
views
Gathering data on bacterial oganism growth conditions
let's say I have a list of organism names like the example below
...
- 13.8k
6
votes
2
answers
2k
views
How to select a cutoff for interaction confidence in STRINGdb?
I have a list of 100 genes that are called as hits in a genetic screening. I want to have a network of the interactions between the proteins of these 100 genes. I am using both STRINGdb web and its R ...
1
vote
1
answer
61
views
How to specify the list of contigs in AGP gap file used for ENA submissions
I am battling the submission of scaffolded assembly to EBI, somehow I can not get AGP gap file right.
background
The only option seems to be using the Webin-CLI submission interface. For the ...
- 5,517
2
votes
0
answers
101
views
PubMed Central Open Access archives are corrupted
I'm trying to download PubMed Central Open Access articles from ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_bulk. However, I am not able to decompress the archives without errors.
...
- 101
1
vote
0
answers
17
views
Ccle miRna data units
Does anybody know what units the mirna expression data on ccle is in? I saw the pipeline in the original paper but it doesn't mention units.
Original paper: https://www.nature.com/articles/s41586-019-...
- 11
1
vote
1
answer
62
views
Question about public availability of human SNP dataset with country of origin
Is there a publicly available data set for humans SNPs, preferably together with the country of origin? If so, could someone please point me towards it.
I've looked through other questions on the site ...
- 1,679