Questions tagged [public-databases]
Use this tag for questions about how to use, download, retrieve, check and browse public databases.
131 questions
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Downloading bulk nucleotide and protein data from GISAID EpiFlu
I am trying to download all influenza protein and nucleotide data from GISAID to process it further in a more friendly environment.
How can I do this programmatically? (or with any method, I am open ...
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NCBI Virus experimentally determined proteins
I am trying to find neuraminidase sequences from influenza virus to work with (as many as possible if not ideally everything available) and I have been using NCBI Virus for this (this is my search ...
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Are there any overlap Between CPTAC-3 and TCGA-HNSC cohorts?
Below is an R code that I used to check for any overlaps between CPTAC-3 and TCGA-HNSC.
From GDC, I downloaded the biospecimen TSV file for Project ID CPTAC-3. Similarly, I downloaded the biospecimen ...
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Is there a database or file containing the type of variant (e.g., if (non-)synonymous, in exon or not) for all human genomic positions?
I'm looking for data which shows the type of SNV variant (at least if the variant synonymous or non-synonymous, and ideally if the variant is in a CDS or not as well) for every variant with respect to ...
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Asterisk wildcard apparently not working for some keywords in PubMed search
For some keywords, adding an asterisk is not increasing as expected but reducing the number of matches in PubMed searches.
I provide here the two issues I have found to date:
The search just for ...
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Finding related Mesh Terms given a substance
Given a list of substance (which can be expressed in any form: general terms or chemical taxonomy) I need to find the specific MeSH term.
I understood that I can use those web services: https://id.nlm....
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How to get Time-Course data for NOS2 & Arg1 Enzymes?
Background: I'm trying to model M1/M2 macrophage switch during a wound-healing process. For a switch from M1 cell population to M2 cell population, there is a reprogramming of the internal metabolic ...
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Databases for mtDNA with location/age
I'm doing some experiments on mtDNA, trying to infer samples' location/age based on the similarity among sequences. I was able to find good samples (with geographical coordinates and age range) for my ...
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Extracting metadata for a list of BOLD BINs
When I view the Public Data Portal page for a specific BOLD BIN, I get some useful metadata, including BIN Details (the image below is from this BIN):
I would like to be able to compile and download ...
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Protein atlas rna-seq vs protein expression region missmatch
I am finding a levels of gene expression in protein vs rna seq not correlating in protein atlas for a gene of interest. In rna-sequencing there is a high level of expression mainly in the brain, in ...
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Is there a database of oligonucleotide duplex sequences and their melting temperatures
I am looking for melting temperatures of oligonucleotide duplexes, but I am having trouble finding data. Can be DNA-DNA, DNA-RNA, or RNA-RNA duplexes, native or modified nucleotides.
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ZINC15 database: proxy server error when trying to download catalog in any format
I am a complete beginner in the use of such databases.
When navigating to the ZINC15 database website and trying to download an entire catalog with the "Download all as" option the request ...
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missing additional visits in GSE data
When downloading GSE data, often I encounter that the authors refer to additional visits in the data description, yet, they are not found in the data.
For example, the following study. They mention ...
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Where would I get the activity profile dataset for Lantus Solostar insulin, and for other diabetes treatments such as Metformin?
I am working on a personal project for a better, more informed management of my own Diabetes Mellitus, Type 2 (aka "T2DM", or "T2D"). With some difficulty I am able to access and ...
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Uploading manifest from CCDI to CGC project
Thank you in advance for your help!
I am trying to download data from the CCDI (Children Cancer Data Initiative) and I have a manifest csv file that I downloaded from the CCDI. I'm trying to upload ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 .. &...
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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 ...
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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.
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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 ...
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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....
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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, ...
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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....
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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 ...
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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 ...
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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 ...
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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, ...
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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 ...
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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, ...
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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 ...
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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 ...
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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 ...
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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"...
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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 ...
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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 ...
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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 "...
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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....
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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 ...
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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.
...
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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-...
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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 ...
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How to identify genes from a genome assembly of C. Elegans?
I have two full genome assemblies for C. Elegans samples collected from two different geographical areas that I found on WormBase. These are in fasta format. I want to go gene-by-gene and compare the ...
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Are there any databases for gene co-expression or expression pattern clustering?
I am currently working on gene clustering based on co-expression pattern in mouse brain. The problem is I do not have some solid way to test my result. Are there any suggestions for databases ...
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