Questions tagged [database]

A repository for data that is organised according to specific rules. Important biological databases include PDB (Protein Data Bank), Ensembl, Uniprot.

Filter by
Sorted by
Tagged with
19 votes
6 answers
3k views

Are there any RepBase alternatives for genome-wide repeat element annotations?

I’m using the RepBase libraries in conjunction with RepeatMasker to get genome-wide repeat element annotations, in particular for transposable elements. This works well enough, and seems to be the de ...
Konrad Rudolph's user avatar
16 votes
3 answers
682 views

Designing a lab NGS file database schema

I am the resident Bioinfo Geek in a hospital academic lab that routinely employs NGS as well as CyTOF and other large volume data producing technologies. I am sick of our current "protocol" for ...
Gus's user avatar
  • 346
15 votes
3 answers
965 views

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?
AlwaysTrying44's user avatar
15 votes
3 answers
7k views

What are the advantages and disadvantages between using KEGG or Reactome?

As enrichment analysis a usual step is to infer the pathways enriched in a list of genes. However I can't find a discussion about which database is better. Two of the most popular (in my particular ...
llrs's user avatar
  • 4,693
13 votes
6 answers
2k views

Converting gene names from one public database format to another

This is a question from /u/apivan19 on reddit. The original post can be found here. I have some proteomics data that was given to me with the UniProt gene identifiers in column 1. I've been trying to ...
gringer's user avatar
  • 13.9k
13 votes
6 answers
401 views

Are there any databases of templates for common bioinformatic file formats?

I want some templates of different file formats that I can use to test my scripts and identify possible bugs in my code. For example, consider nucleotide FASTA, a simple but often abused format, I ...
Chris_Rands's user avatar
  • 3,948
11 votes
5 answers
4k views

How to convert species names into common names?

I’m trying to find common names from a list of scientific names (not all will have them though). I was attempting to use taxize in R but it aborts if it doesn’t ...
Daniel Mead's user avatar
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
  • 9,901
10 votes
1 answer
2k views

How to manipulate protein interaction network from String database in R?

How can I manipulate protein-interaction network graph from the String database using STRINGdb bioconductor package and R? I have downloaded the whole graph for ...
A M's user avatar
  • 103
9 votes
2 answers
176 views

Solutions for managing data in a small bioinformatics / 'omics lab?

A different sort of problem: even a small 'omics lab generates a lot of data, raw, intermediate and processed. What (software) solutions exist for managing this data, such that "old" data can be ...
agapow's user avatar
  • 788
9 votes
2 answers
733 views

How to import a large amount of .bed, .gff, .vcf, .paf, .sam files into an SQL database?

Are there best practices to load different bioinformatics file formats such as VCF, BED, GFF, and SAM to SQL databases? I am wondering how people out there do that efficiently. All of these three ...
0x90's user avatar
  • 1,427
9 votes
1 answer
222 views

How to retrieve logical expressions (KO based) for reactions from KEGG?

The completeness of a module can easily be checked by looking at the Definition entry associated with the module. For example, in module M00010, it is given as: <...
Cleb's user avatar
  • 743
8 votes
2 answers
665 views

Are these standard species abbreviations and how to look up others?

Reactome uses a three letter code for each species which are listed below. Are the letter codes used by Reactome a standard? If so is there a web page or download file that can validate the code and ...
Guy Coder's user avatar
  • 315
8 votes
1 answer
608 views

Publicly available, free, complete database for antibiotics names and classes?

This is a tough one I think: is there a publicly available, up-to-date, free, complete database for antibiotics names and classes? I am specifically looking for information like, e.g., ...
BaCh's user avatar
  • 754
7 votes
6 answers
7k views

How to get a list of genes corresponding to the list of SNPs (rs ids)?

Is there a way for me to get a list of genes given a list of SNP rs ids? I found several questions asked with a similar goal years ago, and the answers are always about using multiple online tools, ...
Haohan Wang's user avatar
7 votes
1 answer
1k views

how to set database other than nr for remote blast+ search

I am attempting to run a BLAST search remotely using BLAST+. I can get search to work correctly at the command line with the following commands: ...
bluescholar1212's user avatar
7 votes
2 answers
46 views

how to find the bound form of an enzyme structure?

For my undergraduate research I'm looking for a database that gives the bound form of a particular protein structure. Is there any database that provide us with such data? So far I've found following ...
Loch23's user avatar
  • 91
7 votes
1 answer
2k views

Where to download JASPAR TFBS motif bed file?

I am interested in determining if any transcription factor binding site motifs are enriched in some BED files from a DNA methylation experiment. I am looking for a database that has BED Files ...
Reilstein's user avatar
  • 367
7 votes
1 answer
421 views

ANY (technical) reason behind submitting sequences to GenBank versus ENA Sequence

The DNA sequence sections of the three INSDC databases (i.e., DDBJ, ENA Sequence and GenBank) are synchronized periodically and strive to keep their stored data as ubiquitously accessible as possible. ...
Michael Gruenstaeudl's user avatar
6 votes
3 answers
95 views

Do any publicly available databases detail protein structure and functional domains?

I am interested in finding a database that takes a gene or protein name as input (possibly with the option to specify transcript) and gives information about the protein's functional domains in terms ...
Dan's user avatar
  • 63
6 votes
2 answers
117 views

Human body sites knowledge base

I'm looking for a lightweight knowledgebase describing the human body to annotate disease sites. I do not need a great level of detail, I just need a kind of basic organs/sub-organs taxonomy. I ...
floatingpurr's user avatar
6 votes
2 answers
379 views

Is there any way of using biopython to write Swissprot files?

I have the following mwe for filtering a Swissprot file based on a certain feature, in this case, transmembrane regions. ...
James's user avatar
  • 409
6 votes
2 answers
702 views

Searching for gene expression data by cell line

I have two cancer cell lines (OCI-Ly18 & riva) that I want to find gene expression data for, but I'm not aware of many gene expression databases that allow searching by cell-line without searching ...
JSneathThompson's user avatar
6 votes
3 answers
158 views

How to find GEO data sets using Drug Bank ID and bioDBnet

I want to find all experiments in GEO that are associated with a drug (for example tolvaptan). Is there any quick and scalable way to to this? I want to query more than 100 drugs. I tried to use ...
hhoomn's user avatar
  • 325
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
6 votes
1 answer
457 views

Where can I find a GWAS data set about genotypes and phenotypes for Zebrafish and rice?

My goal is to work on GWAS method development as a research project. However, human genome data are usually confidential because of the identification problem, so it's very hard to get them. (...
Haohan Wang's user avatar
5 votes
5 answers
217 views

Where is an up to date miRNA database and what happened to miRBase?

miRBase 21 was published June 26, 2014 and was still in its growth phase. Why is it not being updated anymore or the project declared officially dead? ENSEMBL also uses miRBase as a starting point (...
Ido Tamir's user avatar
  • 163
5 votes
2 answers
422 views

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 ...
Arijit Panda's user avatar
5 votes
1 answer
234 views

Obtaining data table headers from GEO using GEOquery

For a study in GEO, I would like to obtain the data table header descriptions, specifically the "VALUE" column for all samples in the study. If you go here: https://www.ncbi.nlm.nih.gov/geo/query/acc....
Ezra Bekele's user avatar
5 votes
3 answers
531 views

KEGG FTP vs KEGG API

I was reading the KEGG plea and I found that it doesn't forbid using the KEGG API. Then, what is in the FTP server license for personal use/academic use that it is not covered by the API? Or I could ...
llrs's user avatar
  • 4,693
5 votes
1 answer
125 views

CRISPR Sequence Finder and Database Download

I am searching for tools to pull CRISPR Spacers from Bacterial Genomes. I am aware of the CRISPRDB and the corresponding identification tool on the web server. Are there other tools for finding ...
Cody Glickman's user avatar
5 votes
1 answer
43 views

How to query a network for a bacterium, specifically Streptomyces caatingaensis or Streptomyces thioluteus?

I have a list of gene/protein IDs and I could not query a network using String, BioGrid, Intact and IIS, for Streptomyces thioluteus. The bacteria I am working with is the Streptomyces caatingaensis. ...
Henry's user avatar
  • 161
5 votes
0 answers
380 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
  • 364
5 votes
0 answers
81 views

Database of Cell Volumes by Cell Ontology?

Are there any databases that have aggregated information on cell volumes? Most useful would be a database keyed by cell ontology (e.g., CL:0000236 for B cell). ...
merv's user avatar
  • 651
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
4 answers
185 views

Database for proteome-wide predictions of protein structures

Accuracies of protein structure predictors have improved quite a lot in recent years. Algorithms such as Rosetta have gotten robust enough to predict structures of large number of proteins. However, I ...
user345394's user avatar
4 votes
1 answer
425 views

Duplicate gene symbol handling in GEO gene expression data

I have downloaded a gene expression data from GEO database (GSE3268) in which in some of its rows there are duplicate gene symbols. For example TP53 exists in two rows with different expression values ...
Majid's user avatar
  • 143
4 votes
3 answers
98 views

Public access to genomics databases

I'm a statistician, and am interested in applying the theory of algebraic Markov models to genomics. Here's one paper I'm interested in: Large-scale genome-wide association analysis of bipolar ...
Puraṭci Vinnani's user avatar
4 votes
1 answer
104 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
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
473 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
4 votes
1 answer
37 views

SARS-CoV-2 sequence used in the AlphaSeq Antibody Datasets to predict binding affinity

Currently we are building a sequence based deep-learning model to predict binding affinity between antibody and antigen. For this we are training a sequence based model with AlphaSeq Antibody dataset (...
Krishna's user avatar
  • 43
4 votes
1 answer
253 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
4 votes
1 answer
113 views

Extracting a cytochrome B sequence from NCBI's nucleotide database

Can someone tell the way to extract the fasta sequences for the gene cytb of Acetes japonicus (shrimp important to China and South Korea)? Can I extract them directly from NCBI nucleotide database (i....
Sofia's user avatar
  • 351
3 votes
2 answers
76 views

Identifying relevant SNPs from a list

I have a list of all SNPs (a list of RsIDs) that fall in the coding sequence of several thousand human genes, and I'm looking for a convenient method to come up with a list of known SNPs that alter an ...
Adrian Smith's user avatar
3 votes
2 answers
162 views

How can I find mutations associated with disease in human histone residues?

I would like to look if there are mutations in residues of human histones associated with any disease. For instance, if a mutation in residue K6 (lysine 6) of histone H2A1A is associated with any ...
plat's user avatar
  • 1,032
3 votes
2 answers
157 views

Difference between clinical significance and statistical significance

I am working on a clinical data analysis project and am from IT domain. While I am analyzing the data, I came to know that though some of the variables are not statistically significant, they are ...
The Great's user avatar
  • 227
3 votes
3 answers
2k 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
  • 2,634
3 votes
2 answers
157 views

Uniprot: Determining protein and organism given a DNA sequence

I would like to find the identity of a protein, together with the organism name and kingdom. The given DNA sequence is below: ...
Mert Metin's user avatar
3 votes
2 answers
108 views

Dataset: Locations of regulatory sequences in the human genome?

I am looking for the positions of annotated regulatory sequences (promoters, enhancers and suppressors) in the human genome. I looked at Ensembl regulatory Build and PAZAR but I am not used to look ...
Remi.b's user avatar
  • 203