Questions tagged [database]
A repository for data that is organised according to specific rules. Important biological databases include PDB (Protein Data Bank), Ensembl, Uniprot.
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What's "signal" in gene expression?
I'm exploring gene expression on public available databases. RefExa is one of the databases I've been studying.
When I searched something there, the website reported the expression value unit as "...
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Information about control data
I am putting this question because I did not find any useful information from internet because of limited access. My question is related to control (or normal) data that we use for somatic mutation ...
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How to download gene expression data from NCBI gene database
In the NCBI gene database, I can add the expression tracks (circled in picture blow) through 'Tracks' button, but How I can download the expression data directly, not just look the picture?
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Digisome generation
I scoured and searched the web for some implementation of digisome creation, but I had a hard time finding any good source code.
By digisomes, what I mean is images with chromosomal masks/borders ...
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Gene expression data in GC-RMA format?
I'm having a hard time retrieving the most expressed genes in a cell line. One of the databases I've found has values for a lot of genes in 60 different cell lines and it seems the data is obtained ...
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Where did the BIND website go?
I was trying to reach the BIND (Biomolecular Interaction Network Database) but the website is down.
Where can I find something similar? Has this platform moved somewhere or what?
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Can second search with limited search space improve result in MS proteomics data?
First, please know that I am a novice in this field and that it is thus very likely that you will regard this question as basic or flat stupid. Please be gentle and don't be afraid to criticize. I am ...
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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 ...
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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 ...
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What would be a reasonable healthy data set/control group to compare with a cell line from TCGA?
Assume I want to run a simple machine learning of healthy/non healthy classification, how can I use TCGA where it has only data of people with cancer. What do usually people do for example for study ...
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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 ...
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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. ...
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How to access organism IDS, taxon nodes from UniProt?
I try to find organism IDs used by UniProt (e.g. 9606 for "Homo sapiens") and information about the 'taxonomic kingdom' this organism belongs to. The only source on UniProt I could find is this file ...
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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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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:
...
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What are the algorithms for biometric identification in large database?
I have been thinking about this problem and reading some related papers for sometime.
The problem can be described as follows:
Suppose that each biometric template is a $d-$dimensional vector. A ...
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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, ...
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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 ...
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How to retrieve InChI key for KEGG compound?
I would like to retrieve the InChI representation for a given KEGG compound but I fail to find a direct solution for this (preferably doing it via bioservices).
One could do it via ChEBI like this:
...
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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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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 ...
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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 ...
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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. (...
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What sequencing data metrics should I record?
I'm new to bioinformatics and Im starting a new microbial sequencing project and I'd like to record all of the qc data correctly. This is research and I'm not sure what I'll need later. Is there any ...
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Is there a way to retrieve ENSEMBL IDs from a search query?
I would like to be able to batch download FASTA files from ENSEMBL. I normally would use the API to download them from the ENSEMBL gene IDs. However, the IDs aren't ones I know, only ones I would get ...
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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 ...
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Genome databases of microbial eukaryotes
I am interested in collecting the reference genomes of marine protists and would like to know which databases can be used for such tasks, and is there a single, centralized database of protistological ...
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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....
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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.
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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:
...
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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., ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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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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 (...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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:
<...
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