Questions tagged [public-databases]
Use this tag for questions about how to use, download, retrieve, check and browse public databases.
116
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Publicly available genome sequence database for viruses?
As a small introductory project, I want to compare genome sequences of different strains of influenza virus.
What are the publicly available databases of influenza virus gene/genome sequences?
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3
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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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13
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3
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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 ...
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3
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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. ...
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2
answers
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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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8
votes
2
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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. ...
- 315
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votes
3
answers
5k
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Retrieve detailed gene descriptions
Given a list of gene IDs, how do you retrieve the gene description, summary and other detailed information in R?
- 2,624
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2
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628
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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 ...
- 179
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votes
1
answer
106
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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, ...
- 1,304
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votes
1
answer
143
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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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2
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2k
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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 ...
- 1,022
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1
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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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6
votes
1
answer
1k
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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 ...
- 273
6
votes
3
answers
335
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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 ...
- 524
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votes
1
answer
2k
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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?
...
user657
6
votes
1
answer
129
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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 ...
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votes
4
answers
275
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How do you query and explore ENCODE data?
I am looking for a modular way to query data from ENCODE.
For example, I would like to get CHiP-seq or similar tracks for a specific cell line. What's the proper way to do it?
Finally, is there an ...
- 1,427
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3
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725
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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 ...
- 153
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votes
1
answer
4k
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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 ...
- 1,304
5
votes
2
answers
381
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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 ...
- 285
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votes
2
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165
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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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1
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37
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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 ...
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1
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292
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Is there a way to import tables in PubMed Central to MySQL or other Relational databases?
I need to use these PMC tables from the medical journals for the purpose of integrating the data with a decision-making software. Though, I can see that one can access full-text for an article from ...
- 201
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answers
356
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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 ...
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55
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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
...
- 51
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0
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267
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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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4
votes
1
answer
1k
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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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votes
1
answer
281
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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4
votes
1
answer
70
views
How to export web NCBI tBLASTn results in table format with many queries?
Context
I'm an MSc student working on writing up my thesis (back home now) from my laptop and, therefore, unfortunately don't have access to a workstation/server capable of doing the tBLASTn search ...
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votes
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221
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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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votes
2
answers
739
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Downloading all COI sequences from BOLD fails
I have metabarcoding sequence data (COI) from bulk animal samples (including arthropoda, nematoda, annelida, mollusca) and I want to BLAST all of these sequences. I used following command to do this: <...
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votes
1
answer
102
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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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1k
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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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1
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489
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Get canonical transcript from UCSC
I am using the following command to get all refseq genes from UCSC:
...
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4
votes
1
answer
447
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Old versions of the reference genome and dbSNP
For benchmark purposes I’m trying to find an old version of the human reference genome (pre-GRCh37) and a matching version of dbSNP.
Unfortunately it appears as though older versions of dbSNP aren’t ...
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69
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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?
...
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4
votes
1
answer
472
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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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246
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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 ...
3
votes
2
answers
131
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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 ...
3
votes
1
answer
312
views
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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votes
2
answers
438
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 ...
- 5,517
3
votes
3
answers
1k
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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).
- 2,624
3
votes
1
answer
70
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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 ...
- 3,100
3
votes
1
answer
50
views
Proteins with one SS bond?
I would like to find proteins with exactly one SS bond. Is there a database where I can search this? I've tried advanced search on https://www.rcsb.org/, but no such option, at least I could not find ...
- 205
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votes
1
answer
46
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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votes
1
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248
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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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votes
2
answers
95
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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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votes
1
answer
117
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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
<...
- 131
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votes
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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, ...
- 131
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votes
1
answer
73
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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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