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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42 views

Scientific names of taxids with kraken 2.0.8 beta, command kraken2 --use-names error

I am running kraken 2.0.8 beta to do taxonomic classification of micorbiota data coming from a MinION run based on the 16S gene. To do so I am using the pre-bult kraken SILVA database. I managed to ...
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How can I open the 16S_silva.installation.sh in kraken2?

I installed kraken2, which includes the 16S silva database. Indeed I see 16S_silva_installation.sh. How ca I install it?
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Marked sequence search on genomes [closed]

Where does one gets fullest influenza database and 2019nCov? How does it looks like? It's just a string? I have an idea, I want to correlate virus with existing viruses that have vaccines. I could ...
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58 views

Vegetable databases usage

Good morning, I'm aligning with blast some species, against all nt database to analyse the vegetables. However, in some cases we have species of animals mixed with vegetables and want only to detect ...
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27 views

Median for clinical 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 ...
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1answer
22 views

Use of Electronic Phenotype in EHR

May I know what's the use of Electronic Phenotyping using EHR data? I did refer this link but have few questions I understand that ...
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Search for XL-MS datasets

I am looking for human cross-linking mass spec datasets, where the exact residues that were crosslinked are stated. Any format, say csv, ...
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1answer
27 views

How to extract hypervariable region of mitochondrial dna from its fasta file?

Recently I've done some analysis on Human mitochondrial DNA and now I want to run the same analysis on only hypervariable regions of mitochondrial DNA to see whether the changes that I have observed ...
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1answer
50 views

Are there genomics databases for neurological and psychiatric disorders?

Are there databases that relate genetic disorders with neurological disorders? I am thinking of something like COSMICS for cancer? AFAIK cancer usually develops due to a combination of 5-10 ...
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Extract sequence from nucleotide databse

Can someone tell the way to extract the fasta sequences of gene Cytb? Can I extract them in the nucleotide database? For instance, I'm trying to fetch the fasta data of Acetes japonicus of cytb gene. ...
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Blood analysis devices: how and where is the data saved

I've read that there are blood analysis devices that can automatically determine the data for each specified analyse. You can expect to get the results in less than a day. Q: How and where do they ...
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Calculate the percentage of the genome that is represented by some sequences

I have construct a repeat libraries using de-novo identification methods. All results from different tools has been combined into one fasta file. How can I get the percentage of how much these ...
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How to apply RDP, Greengenes and other special taxonomies in Krona?

I used Kraken 2 to classify my 16S metagenomic data using both RDP and Greengenes database. As these are special databases the taxonomic ids assigned do not match with the NCBI taxonomic ids. I found ...
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50 views

Are there databases to annotate non-coding mutations?

I would like to ask if there are some known databases that allows to annotate non-coding mutations in a given region for the human genome? Preferably, if the database is downloadable so I am able to ...
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93 views

How to obtain the standard gene name

I have a list of genes and proteins extracted from literature. How can I convert them into standard gene names.
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73 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 ...
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Where to find secondary metabolites in lichen (and herbal medicine)? [closed]

I've searched around and found about 80 specific secondary metabolites for lichen, but I can't seem to find anymore. They were mostly from research papers. I read that there are more than 800 ...
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how to create database and taxonomy for arsM amplicon analysis

Could you please guide me on how I can create the arsM database and taxonomy like 16s data for the arsM gene using the primer set. I need to analyse the arsM microbial diversity using amplicon ...
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Store and search on variant and annotation data

I need to store a large number of variants with their annotations. I need to import dbSNP, as well as Clinvar, and ExAC etc. Also I have sample variant data from patients. I need to be able to search ...
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Need help in identifying origin of variants in CIVIC

We usually denote the origin of a mutation as either somatic or germline. This information is usually available in certain databases such as CIVIC, ClinVar, COSMIC etc. But when we come to variants ...
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1answer
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Merging transcriptomes coming from different experiments

I'm planning to build a transcriptome by pooling all existing transcriptomes in SRA for a non-model species (which has no reference genome) to study differentially expressed genes and the like. It ...
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1answer
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Find similar proteins with similar tertiary structure?

I'm a mathematician studying knotted curves and am trying to find some applications of my work in proteins. Using https://www.rcsb.org/, how do I find proteins that have similar (but perhaps not the ...
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1answer
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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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48 views

Restriction enzymes with multiple recognition sequences

In a bioinformatics programming course I am currently teaching (using Python, and approached from a mostly CS rather than a biology background) I assigned a project which involves finding sites where ...
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How to use analysis output in my pipeline

I am running an analysis and I want to edit the output that I received from that analysis. However I cannot define the output name in my pipeline, because after running the analysis it is asking me to ...
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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 ...
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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). ...
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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. ...
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List of human transcription factors

I'm looking for a list of human transcription factor (TF) genes. Where can I find a TF database or how can I retrieve this list from other databases?
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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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Does anyone have older versions of NT and 16s RNA DB from NCBI?

I am in search of past years' versions of NT and 16s databases from NCBI. I recently contacted NCBI about this and they replied: Unfortunately, we do not archive past versions of the blast ...
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511 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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Why is Clostridium difficile toxin A + B outdated in snomed?

I'm looking at the new version of the Snomed dictionary and the concept 707993000 Clostridium difficile toxin A + B (substance) is deactivated (and outdated) since ...
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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 ...
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233 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 ...
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Where can I find the DNA sequence of the C. elegans rRNA cluster?

Where can I find the DNA sequence of the C. elegans rRNA cluster? Ideally, I would be able to do it using the command-line. I've tried using NCBI but the results are unsatisfactory. I am interested ...
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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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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 ...
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209 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 ...
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Blueprint replicates

On Encode, it's pretty easy to find out replicate information about the experiments, however I am having some difficulty finding this information on BLUEPRINT DDC, at http://dcc.blueprint-epigenome.eu ...
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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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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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536 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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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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101 views

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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51 views

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 went?

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?