Questions tagged [public-databases]

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

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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: ...
Robvh's user avatar
  • 133
1 vote
0 answers
135 views

How to (efficiently) search nuccore to retrieve only annotated sequences?

I wish to efficiently search nuccore to retrieve only annotated sequences. By "annotated" I mean that the nuccore entry contains annotation information. An equivalent definition (if I understand ...
Oren Milman's user avatar
1 vote
0 answers
68 views

Is there a built-in parser for the textual feature table that Entrez.efetch returns?

Entrez.efetch helpfully gives me the feature table of a nuccore entry. If I understand correctly, efetch can only return the ...
Oren Milman's user avatar
4 votes
2 answers
736 views

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: <...
Robvh's user avatar
  • 133
1 vote
1 answer
227 views

Available phenotype data from GTEx

I am using gene expression data from the The Genotype-Tissue Expression (GTEx) project, available here: http://gtexportal.org. I would also like to use phenotype data for each sample (especially age, ...
Sylvia Rodriguez's user avatar
5 votes
0 answers
354 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 ...
rtviii's user avatar
  • 342
2 votes
1 answer
1k views

How to download RNAseq gene expression data from GTEx

I would like to download RNAseq gene expression data from GTEx from the liver only. What is the best way to do this? I have tried a few things. I downloaded several files from the GTEx website (https:...
Sylvia Rodriguez's user avatar
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 ...
d33tah's user avatar
  • 151
1 vote
2 answers
87 views

Appropriate value to replace outliers in clinical studies

I am working on clinical study where I am focusing on binary classification problem. There are few variables which has outliers. I am trying to know which would be the right value to replace ...
The Great's user avatar
  • 217
1 vote
0 answers
33 views

Human Cell Atlas - cell annotations

Human Cell Atlas Preview Datasets have been available for a while now (there was some discussion about that earlier). However, although the raw data is available, cell labels are not (for example, ...
burger's user avatar
  • 2,169
1 vote
1 answer
45 views

Are there databases or resources that contain expression of proteins or genes before and after cancer treatment?

Are there databases that contain information about gene or protein expression before and after targeted therapy or chemotherapy? I am curious about different cancer cell lines or cancer types. Any ...
0x90's user avatar
  • 1,427
2 votes
2 answers
133 views

Looking for a taxonomic dataset that links tree genera (or species) to families

I am looking for a taxonomic dataset that would allow me to links tree genera (or species) to families. In particular, I am interested in the tropical species found in the Amazon. I found a long but ...
Davide Leonessi's user avatar
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 ...
Jake B.'s user avatar
  • 205
4 votes
1 answer
444 views

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 ...
Konrad Rudolph's user avatar
1 vote
1 answer
32 views

Is there a resource where I can donwload E. coli assemblies grouped by their pathotypes?

I will preface this by saying I'm not a microbiologist, so I apologise for any haziness and I'll be happy to expand. I would like to download the assemblies of different E. coli genomes and group ...
TW93's user avatar
  • 449
2 votes
1 answer
245 views

How can I get plant Genome size, total number of genes, EST, and chromosomes number

How can I get plant Genome size, total number of genes, EST and chromosome number from phytozom and plantDB?
Imran's user avatar
  • 21
5 votes
4 answers
272 views

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 ...
0x90's user avatar
  • 1,427
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 ...
user3883's user avatar
5 votes
1 answer
289 views

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 ...
PinkBanter's user avatar
1 vote
1 answer
130 views

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 ...
Slepecky Mamut's user avatar
3 votes
3 answers
1k 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).
Peter's user avatar
  • 2,624
3 votes
1 answer
73 views

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... ...
ljs's user avatar
  • 265
2 votes
3 answers
63 views

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 ...
Scientist's user avatar
  • 111
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 ...
Sam 's user avatar
  • 51
4 votes
1 answer
470 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 ...
Đorđe Relić's user avatar
0 votes
2 answers
236 views

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 ...
ImAUser's user avatar
  • 11
3 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 ...
RJF's user avatar
  • 181
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 ...
jaslibra's user avatar
  • 524
0 votes
1 answer
33 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 ...
Satwik's user avatar
  • 101
4 votes
1 answer
245 views

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 ...
blehblehblecksheep's user avatar
1 vote
1 answer
434 views

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 ...
William Tenorio's user avatar
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 ...
Obinoscopy's user avatar
2 votes
1 answer
260 views

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". ...
eric_kernfeld's user avatar
4 votes
1 answer
102 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 ...
JSneathThompson's user avatar
2 votes
1 answer
83 views

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'...
Reilstein's user avatar
  • 367
4 votes
1 answer
1k 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://...
niraito's user avatar
  • 41
4 votes
1 answer
279 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]%...
bli's user avatar
  • 3,100
1 vote
0 answers
24 views

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 ...
Imer Muhović's user avatar
6 votes
1 answer
236 views

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 ...
Gregor Sturm's user avatar
2 votes
1 answer
771 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 ...
ShanZhengYang's user avatar
3 votes
1 answer
248 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 (...
Ian Sudbery's user avatar
  • 3,301
6 votes
1 answer
1k 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 ...
Gregor Sturm's user avatar
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 ...
terdon's user avatar
  • 9,662
7 votes
2 answers
626 views

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 ...
Zubo's user avatar
  • 179
3 votes
1 answer
70 views

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 ...
bli's user avatar
  • 3,100
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 ...
terdon's user avatar
  • 9,662
2 votes
1 answer
58 views

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 ...
Loch23's user avatar
  • 91
7 votes
3 answers
5k 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?
Peter's user avatar
  • 2,624
5 votes
1 answer
4k 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 ...
Mark Ebbert's user avatar
  • 1,304
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. ...
floatingpurr's user avatar