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Questions tagged [public-databases]

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

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ncbi…eutils/esearch.fcgi: How to search now in the snp database?

According to the 2017(!) textbook, it worked at that time, for instance, https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=snp&term=autism At ...
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Where can I find hemagglutination inhibition (HI) assay data?

I am looking for hemagglutination inhibition assay data for type A influenza virus. Could someone please give me a link to a database with this information? Thanks.
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2answers
50 views

Receptor-ligand database

How can I find ligands of receptors (or vice versa)? For example, I want to find the receptors of IL-8 (CXCL8).
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How to query the Human Microbiome Project (HMP) to find all subjects with both 16s and WGS workups?

I am looking for a query to run on the HMP database that will return all subjects who have had BOTH 16s and whole genomes sequence (WGS) workups. I am currently using this query... ...
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Best data repository to publish a large 'plotly' table containing all annotations on a transcriptome?

I am not sure whether this is the best SE community for this question. I want to publish a transcriptome paper, along with interactive materials enabling readers to peruse the data behind the ...
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Gathering data on bacterial oganism growth conditions

let's say I have a list of organism names like the example below ...
3
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1answer
44 views

Get results of keyword search on Pfam via python script

I'm interested in all proteins that are in any way associated with Danio rerio. I decided to look them up at Pfam data base and when I just make a keyword search, I get a a nice list which looks like ...
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1answer
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GDC data portal cancer subtype

I need to use Gene Expression quantification data (using HTSeq-FPKM-UQ) for breast cancer data on the gdc portal (https://portal.gdc.cancer.gov/repository) to classify breast cancer subtypes (luminal ...
2
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1answer
29 views

Where to download baseline/average gene expression level of all human coding genes?

I am looking for the most appropriate dataset for downloading baseline gene expression level across all human coding genes during development. I am aware that EMBL Expression Atlas is one of the ...
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Find the date that sequencing was performed

I've got a bunch of RNAseq datasets from ENCODE and I'm looking to identify variables contributing to variance among my samples. For example, is there any easy way to find out the precise date which ...
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1answer
26 views

What are some good sources of 3rd order gene expression data

I need good sources of gene expression data in the form of 3rd order tensors. Typically the commonly available datasets are in the form of a matrix, for instance, $sample \times gene$ or $gene \times ...
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Is there a database of protein sequences/structure along with their melting temperature?

Such databases have been constructed for example in here or here. But I can't find them anywhere online. Can someone point me to where I can find one available online? Otherwise I'll have to write to ...
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How to download SNP data from specific regions, population and positions?

I am totally new in Bioinformatics and I would like to apply my knowledge in feature selection on the tag SNP problems. To do that, I've read a lot of papers and books in order to understand the main ...
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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 one which is exploratory in nature. Intend using the different ...
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1answer
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Convert CD (cluster of differentiation) into gene symbol

I want to convert names according to the "cluster of differentiation" nomenclature into accepted gene symbols. For example, CD3 should map to "CD3a;CD3b;CD3c;CD247" and "CD45RO" should map to "PTPRC". ...
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1answer
23 views

Human SNP databases other than dbSNP

I'm working on a project to identify variants as being either germline or somatic based on nearby SNPs, and I was wondering if there were any databases of SNPs for Homo sapiens other than dbSNP? I'm ...
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1answer
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How to add data to AnnotationHub

I recently started using the Bioconductor AnnotationHub package for accessing lots of common datasets, but I've noticed that there are a lot of newer databases that have not made it into AnnotationHub'...
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1answer
139 views

A Database for Plant Metabolome or Secondary Metabolites?

I am searching for a plant metabolome or secondary metabolite database for a college bioinformatics project. Up until now, I have found these two databases, as I am giving their links below; http://...
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1answer
106 views

How can I reproduce a manual NCBI search with Biopython Entrez module?

I'm trying to make a Biopython script that reproduces a manual search on the NCBI website. My manual search gives me the following URL: https://www.ncbi.nlm.nih.gov/nuccore?term=ANOS1[gene%20name]%...
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Can I upload only co-assemblies to ENA, using existing ENA samples?

Lets say I am using reads downloaded from ENA, assembling them and doing further downstream analyses. Would it be possible to then upload the results of the co-assemblies and other analyses back to ...
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Human Cell Atlas - Data availability

A news item from 2017-10-18 on the website of the Human Cell Atlas states: In addition, the consortium today also announced the impending release of gene expression profiles from the first one ...
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1answer
73 views

Downloading an open-source MAF with tumor and normal BAMs?

I'm writing an R package that manipulates MAF files. Normally, I generate a small example of a file and use this for testing. (e.g. a subsetted BAM or MAF). In this case, I would need a MAF and a ...
2
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1answer
43 views

Database of position weight matrices for protein motifs?

I am trying to identify proteins that carry a consensus target sequence for a kinase. Usually if I am working with, for e.g. transcription factors binding to DNA I would use position weight matrices (...
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1answer
134 views

What is the ICGC normalized_read_count?

I downloaded gene expression data (exp_seq) from the ICGC file browser. For each sample and gene, the file contains a ...
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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 ...
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2answers
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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 ...
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1answer
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Automating sequence download from Wormbase

I'm working on the C. elegans model organism, for which there exists an online biological information database: Wormbase. I'm able to manually search for a transcript (say "K06C4.12") and this gets ...
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2answers
171 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 ...
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1answer
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How can I compare structures of proteins responsible for dehydration tolerance in plants?

For my undergraduate research project, I'm trying to compare the structures of some proteins, specifically transcription factors crucial for dehydration tolerance in plants, in the hope of finding ...
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2answers
546 views

Retrieve detailed gene descriptions

Given a list of gene IDs, how do you retrieve the gene description, summary and other detailed information in R?
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1answer
578 views

hg38 GTF file with RefSeq annotations

I'm not sure what I'm missing, but I'm struggling to find an official hg38 GTF file with RefSeq annotations. I'd like to provide ...
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2answers
1k 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. ...
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3answers
188 views

How to determine the primary Uniprot accession number from a set of accession numbers?

Given a list of Uniprot IDs that are linked to an Ensembl gene ID, is there a way to systematically determine the UniProt accession corresponding to the protein product of the gene's primary ...
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1answer
174 views

Missing data mappings in mygene.info while trying to convert Genes Ensembl Ids to Entrez Ids

I need to convert a lot of Ensembl Ids to the relative counterpart in Entrez (e.g., ENSG00000157764 > 673). I found mygene.info ...
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1answer
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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 ...
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1answer
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Database of copy number alterations in different cancer types

Is there a database of somatic copy number alterations (CNAs) in different cancer types? That is, annotations of which CNAs are more commonly seen in different cancer types.
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Where can I find summary data for how common certain mutation *types* are?

I'd like to know how common certain mutation types are in public data sets like the 1000 Genomes, ExAC, and ESP6500. Specifically, I'd like to know the distribution of stop-gains, stop-losses, ...
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3answers
124 views

Secretome and membrane receptor profiles

I am looking the secretome profile and the membrane receptor profile for a given cell type. In my specific case, this should be the secretome and outer membrane receptor profiles of dorsal root ...
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1answer
186 views

Get canonical transcript from UCSC

I am using the following command to get all refseq genes from UCSC: ...
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1answer
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Is Wikidata a reliable KB for genomic and drugs annotations?

I'm looking for a Linked Open Data approach to annotate a dataset with human genome and drugs information. According to the Linked Open Data cloud, there are a lot of interconnected ...
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3answers
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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 - ...
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1answer
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What is a good pipeline for using public domain exomes as controls?

I'm currently attempting association analysis with an extremely small set of patient exomes (n=10), with no control or parental exomes available. Downloading the ExAC VCF of variant sites (http://exac....
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2answers
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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 ...
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3answers
779 views

Publicly available genome sequence database for viruses?

As a small introductory project, I want to compare gene sequences of different strains of flu virus. Are there publicly available databases of flu virus gene sequences?
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3answers
279 views

How to extract RNA sequence and secondary structure restrains from a PDB file

I'm trying to find a programmatic way to automatically extract the following information from a PDB file: RNA sequence Secondary structure restraints in bracket format, e.g. ...
5
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1answer
268 views

Entrez or Ensembl gene IDs?

I'm using several datasets that are encoded using either Entrez or Ensembl IDs to specify genes, and need to decide on which to standardise on. Are there any major reasons to use one over the other? ...
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3answers
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Given a VCF of a human genome, how do I assess the quality against known SNVs?

I'm looking for tools to check the quality of a VCF I have of a human genome. I would like to check the VCF against publicly known variants across other human genomes, e.g. how many SNPs are already ...