Questions tagged [public-databases]

Use this tag for questions about how to use, download, retrieve, check and browse public databases.

Filter by
Sorted by
Tagged with
0 votes
0 answers
15 views

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 ...
msun5040's user avatar
1 vote
1 answer
29 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 ...
ricardo3889's user avatar
0 votes
0 answers
17 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 ...
ricardo3889's user avatar
1 vote
0 answers
51 views

Need help with binding DB API

...
Neeleshwar Pandey's user avatar
1 vote
1 answer
29 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 ...
Harry Richman's user avatar
5 votes
2 answers
266 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 ...
jay.sf's user avatar
  • 173
1 vote
2 answers
108 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 ...
HelpNeederStudent's user avatar
4 votes
1 answer
235 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 ...
AppleBees's user avatar
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 ...
KirkD-CO's user avatar
  • 175
1 vote
1 answer
65 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 .. &...
c00kieRaptor's user avatar
0 votes
0 answers
34 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 ...
llrs's user avatar
  • 4,693
1 vote
1 answer
50 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. ...
Sudoh's user avatar
  • 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 ...
Soerendip's user avatar
  • 1,295
2 votes
1 answer
406 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....
719016's user avatar
  • 2,324
1 vote
1 answer
53 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, ...
ning's user avatar
  • 141
1 vote
0 answers
155 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....
Jatin Kashyap's user avatar
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 ...
A.Dumas's user avatar
  • 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 ...
h3ab74's user avatar
  • 836
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 ...
microbeprincess's user avatar
2 votes
0 answers
219 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, ...
Elisa's user avatar
  • 21
3 votes
2 answers
504 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 ...
Kamil S Jaron's user avatar
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, ...
Tomaž Bratanič's user avatar
3 votes
2 answers
142 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 ...
pietro_molina's user avatar
2 votes
0 answers
83 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 ...
Muhammad's user avatar
0 votes
1 answer
208 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 ...
HelpNeederStudent's user avatar
2 votes
1 answer
458 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"...
Kenneth's user avatar
  • 21
1 vote
1 answer
259 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 ...
alex3465's user avatar
  • 151
0 votes
1 answer
29 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 ...
variancekills's user avatar
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 "...
pietro_molina's user avatar
3 votes
2 answers
98 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....
Sk Sarif Hassan's user avatar
1 vote
1 answer
67 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 ...
Kamil S Jaron's user avatar
2 votes
0 answers
103 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. ...
TomTom's user avatar
  • 121
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-...
n232's user avatar
  • 11
1 vote
1 answer
63 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 ...
user257566's user avatar
1 vote
1 answer
115 views

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 ...
Jabbath's user avatar
  • 113
1 vote
1 answer
43 views

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 ...
jasperhyp's user avatar
3 votes
1 answer
126 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 <...
Knio's user avatar
  • 131
6 votes
1 answer
129 views

How to search for high coverage SRA entries

The Question I want to find high coverage SRA entries, e.g., above 100x. I guess the best way is to use https://www.ncbi.nlm.nih.gov/sra with an appropriate search term. I don't mind if the search ...
Oren Milman's user avatar
0 votes
1 answer
952 views

OpenAPI-Generator Python Client Instructions Examples

Trying to learn a little bit of Python and Biopython I ended up figuring out what a Rest API is when the RCSB PDB repository released its new Rest API. I tried to retrieve info from the PDB repository ...
pippo1980's user avatar
  • 1,043
1 vote
0 answers
12 views

Drug classification database information

Is there any database that give information about the drug class. Right now I have all the MeSH id of the drugs from different publications. So right now I'm looking one by one drug looking at the ...
kcm's user avatar
  • 1,804
0 votes
4 answers
170 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? ...
gbrlrz017's user avatar
1 vote
0 answers
32 views

Fastq dataset after clustering

I'm doing a project for DNA archival storage systems Is there an open-source dataset used as ground truth for clustering? E.g A file containing the ground truth strand sequences, which have been ...
Brian Formento's user avatar
2 votes
0 answers
315 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 ...
kcm's user avatar
  • 1,804
3 votes
2 answers
183 views

Where can I find the genotype frequencies for the SNP's that are tested at 23andMe, Ancestry and FTDNA/MyHeritage?

I want to add the frequencies of the genotypes to a baseline of raw DNA data I've got from the DNA testing companies 23andMe, Ancestry and MyHeritage (tested at all). All in build 37 human genome. ...
a4xrbj1's user avatar
  • 139
1 vote
1 answer
68 views

How to compact variant data to their genes without bias?

I have a dataset of genes I am trying to collect data on from public databases, to use as features in machine learning. I am trying to take some features from UCSC genome browser (e.g. number of CpG ...
DN1's user avatar
  • 45
0 votes
1 answer
101 views

europmc and tidypmc R library for extracting or making metadata from publication

I'm trying to use this europmc r libray where I have a list of pmids to look for. I tried with pubtator but its bit complicated.In Europmc i can all the annotated terms etc. ...
kcm's user avatar
  • 1,804
2 votes
4 answers
572 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: ...
An Ignorant Wanderer's user avatar
4 votes
1 answer
95 views

Where can I find lncRNA expression data for different cell types?

Are there any publicly available databases providing expression data for long non-coding RNAs (lncRNAs) across cell types of multicellular organisms? Alternatively, are there lesser known UCSC tracks ...
Gawain's user avatar
  • 315
0 votes
1 answer
38 views

Determine if an organism is microbic or unicellular

I am doing some metagenomic analysis of samples which can only contain microbes due to the experimental setup. For this, it would be useful to be able to distinguish whether a specific organism is a ...
Wrzlprmft's user avatar
  • 101
1 vote
0 answers
24 views

How do protein-protein interaction databases work?

I am a student and just trying to gain a base level understanding of PPI databases and how to interpret their data. For example, when inputing multiple genes into String, does it only give protein-...
DN1's user avatar
  • 45