Questions tagged [database]

Questions pertaining to organized collections of biological data.

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Resource to obtain listings of tissues that different viruses infect

I am working on a project that involves analysis of viral DNA sequences. I'd like test hypotheses about issue specificity. Ideally I'd be able to get a table of virus/strain names with a column in it ...
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Datasets for Polymerase Cycling Assembly

I am currently studying Polymerase Cycling Assembly. I would like to find examples (or datasets) of sets of oligonucleotides that are effective for PCA. It would also be good to know of sets that ...
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2 answers
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Where can I get info about A. thaliana proteins' locations?

I have a list of A. thaliana proteins and I'd like to know their location in the cell. I've found SUBA but they seem not to share their dataset and only allow queries through their website. It's ...
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How to customize the output of my BLASTP output form

I'm trying to align the output of I got previously to against the swissprot database, and I need to have an output in tabular form with ...
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1 answer
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What structures does our brain use for a quick indexing of all the data we store in our heads?

What structures does our brain use for a quick indexing of all the data we store in our heads? From how my brains work (i.e. that I can very quickly recollect something from the past) I would say that ...
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Are there any online resources that have a list of post-translational modifications and their molecular weight?

I am studying a protein and I am interested in learning about all the post-translational modifications that it has (as I am analysing it via Western blot). I have found a list of the post-...
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How to find a model organism's standard data about proteome size and genome size?

I want to know proteome size(the number of proteins not length) and genome size(length) of model organisms like Caenorhabditis elegans, Saccharomyces cerevisiae etc. I found www.uiprot.org and I made ...
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1 answer
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Are there any online resources for finding the signaling pathways that two proteins both belong to?

I am studying the proteins GSK3 and AMPK and I am trying to identify the signaling pathways that both of these proteins belong to. From reading journal papers I have found out that both of these ...
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-4 votes
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Finding All of the Genes in a given Genome

I'm interested in finding the start position of each nucleotide in a given genome. I first went to EcoCyc and wrote a scraping script for their E coli data, but I can't find the same web page layout ...
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Looking for study/genome data for HIV in different organs

I am looking for a research study or data base that has HIV genome data available in fasta or similar format. Specifically I need genome data of HIV taken from different organs in the same subject. I ...
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3 votes
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Is there a taxonomy of species with emergence and extinction dates?

I know the NCBI has a list of each species and their place in the evolutionary tree. But do they have the dates that these species existed? Does any such database (partial or complete) exist anywhere? ...
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Source for Specific Models of Birds' Habitat Suitability

This source gives a very detailed analysis of what habitats are best suited for many different species. However, this is a government funded project and, to the best of my knowledge, not published in ...
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Advice on type of database and software for research on genetic diversity of crops

for a research project I am evaluating the potential of Robusta coffee genetic resources in the tropic region of Africa. Different ex-situ genetic lines will be mapped as well as chemical, ...
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2 votes
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What websites biologists use to check what new plant or animal species have been discovered in the world?

What are the databases or websites that biologists use to check what new plants or animals have been found in the world? The service should list the location of the discovery, time of discovery, image ...
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3 votes
1 answer
633 views

Where can I download a list of all plant species of the world?

Where can I download a complete list or dataset of every plant species in the world?
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How can I search through literature databases for words containing a * when the asterisk is read as syntax and not part of a query?

I'm exploring the literature on microRNA, where it is common for the less utilised strand of the miRNA duplex to be referred to as the miRNA* strand. However, I am experiencing some issue searching ...
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Public fermentation/cell cultivation database?

I am wondering if there are any large collections of fermentation or cell cultivation data publicly available. I am interested in all cell types used within industrial biotech and biopharma, ...
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Cell image database for citotoxicity test

Is there any cell image database for citotoxicity tests? I know that there are several image databases available (like this, this and this one), but none of them have the images for citotoxicity tests....
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Is there any animal database or website that classifies animals as wild / domestic?

Is there any animal database or website that classifies animals wild / domestic? Or.. the site that I can get the wild / domestic information of animal list...
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5 votes
1 answer
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Where can I find SARS-CoV-2 genome sequences for the UK?

I have downloaded and analysed the sequences of 832 complete samples from the European Nucleotide Archive but I cannot find a single one that was from the UK. I have also tried Genbank and they do not ...
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1 vote
1 answer
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Image Dataset for Cardiac cells for Mus musculus?

I'm working on developing a transfer learning model to detect cells in a culture using microscopic images. for that i require data set of images having microscopic images of various cell types. Is ...
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1 vote
2 answers
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An online tree of life with extinct species present?

There are awesome online phylogenetic trees such as OneZoom. But they all only list living species. I want to see dinosaurs between birds and crocodiles. I wanna see that humans are reptiliomorphs ...
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-1 votes
3 answers
222 views

Where are there analyzable signed directed network datasets?

I'm looking for biological datasets with specific properties that are available for me to analyze. Informally put, I have a hammer and I am looking for a nail. That is to say, I have an algorithm and ...
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Large study showing that attraction to only the same sex has to do with your genes, published where?

Can someone please help me out and find and link me the study from a couple of years ago that showed how only same sex attraction, when the male cant become attracted to a woman, it has to do with ...
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1 vote
1 answer
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In the notch signaling pathway, what is Fringe activating?

Take a look at the notch signaling pathway in human from KEGG : https://www.genome.jp/kegg-bin/show_pathway?hsa04330 I want to know what is Fringe activating. It is not pointing to another gene or ...
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Is there any program or website that allows me to create phylogenetic trees without having to insert an already created dataset?

I asked a similar question on Quora before, but did not get any useful answers as the program the one answerer suggested turned out to have the exact same problems as all others I have found so far. ...
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1 vote
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Meiotic recombination hotspots

Im trying to find a proper and general file with chromosomal coordinates for meiotic recombination hotspots. I know that ucsc hgtables, has a table with recombination regions and their recombination ...
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3 votes
1 answer
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How to get a list of kinases that phosphorylated a particular protein?

I am analysing the protein SF2 (also named as SRSF1). In the database, it is shown that this protein is often phosphorylated at the 189th tyrosine residue. I want to know which proteins could have ...
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1 answer
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Do conservation oriented genetic database exist?

Are there any projects for the creation of the international genetic database of all endangered species, so we, at least, have a chance to clone them in the future if our current conservational ...
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Database for Macroinvertebrate Taxonomy

I compiled different data sets of invertebrate occurrences across some countries and now I want to ensure that all the taxonomic information is homogenized and correct. To this end, I am looking for a ...
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Database of colors mapped to species

I was wondering about the physics of color, and now am interested in finding out if there are any resources (databases, text files, html tables, or pdf listings) of species and their associated colors ...
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Which database has the ready made 16S rRNA Multiple Sequence Alignment File that I can download directly from?

In my case, I need the ready made 16S rRNA Multiple Sequence Alignment File for E.coli and use it to generate the phylogenetic tree file in Newick format. I've tried using the one from utexas website, ...
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1 vote
1 answer
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16S rRNA and 5S rRNA datasets

I need 16S rRNA and 5S rRNA (Gammaproteobacteria - E.coli) Secondary structure files in ct format. I tried looking for them in different RNA databases, could not find one. Can someone tell me where ...
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3 votes
1 answer
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How to interpret this PubChem record of L-Alanine

Using the PUG service from NCBI, I am retrieving 3d structure data for a molecule. Raw data here. I am trying to understand this record, specifically for the purpose of rendering in a 3D coordinate ...
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1 vote
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Open database of whole slide digital pathology images

I am looking for sequential image sections (stacks) of biological structures (such as liver, kidneys etc.) that I can download and use. Most of the pathology images I have found are either one image ...
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18 votes
3 answers
2k views

Public database of animal specifications

I'm a math teacher looking for data to help my students interested in biology complete a quantitatively flavored study of animals. (As a math person, I apologize if I'm not using discipline-...
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5 votes
1 answer
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Where are the statistics for vaccine side effects?

My son told me that that during a discussion at school someone mentioned statistics about side effects of vaccines (I assume that the discussion was about standard vaccines in France). The numbers ...
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1 vote
1 answer
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Open Mass Spec Database

Wondering if there is an open (freely available) database of Mass Spec Data, particularly for the Substances/Compounds listed in NCBI. Specifically, I am not sure if NCBI includes the mass ...
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  • 543
2 votes
1 answer
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Comprehensive database of cell types

Wondering if there is a comprehensive list/database of cell types, similar to this wiki list of cell types in the human body. It lists probably 100+ different types, but this is just for a human. If ...
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0 votes
1 answer
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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. I've checked in databases such as fludb.com, however it seems to only have genetic data. A lot of the time, ...
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2 votes
0 answers
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Where to find fossil databases [closed]

Looking for sites with fossil data in the following categories. Fossil cells Fossil invertibrates Fossil fish Fossil amphibians Fossil reptiles Fossil dinosaurs Fossil birds Fossil mammals Fossil ...
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1 vote
1 answer
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List of genes across species (or just for humans)

Wondering if there is a place that has a list/table/database of all the genes in the human genome, and/or all the known genes in all the species we've studied so far. Something that contains any of ...
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1 vote
2 answers
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Tree of Life in Text Format

Wondering if there is a tree of life in Text format for open data sharing.
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3 votes
2 answers
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Is there a publically available database of microbes that details what their wastes and food sources are

Is there a publically available database of microbes that contains what their wastes and chemical food sources are in addition to other traits. So that I could do like a sorted search for microbes ...
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5 votes
2 answers
564 views

List of proteins by number of amino acids / chain length

Is there any protein database online where I could obtain a list of proteins ordered by the length of their chains / number of amino acids, starting from the shortest, as well as to see their amino ...
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1 vote
1 answer
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Mouse H2 allele sequences

I've been trying to find complete sequences of mouse (Mus musculus) MHC H2 locus haplotypes for quite some time now with limited success. The EBI IMGT database has a table of mouse H2 haplotypes, yet ...
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1 vote
1 answer
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Where do I get an annotation file for yeast genome with ENSEMBL ids?

Even the annotation files hosted on the Ensembl site have systematic names (starting with Y..) instead of ENSEMBL ids (starting with EN..). I bet there would be a place where I can get an annotation ...
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3 votes
0 answers
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How to interpret the relationships of PTMs from BioGRID's data

On BioGRID Database, PTMREL is a file that describes relationships of the PTMs (Post Translation Modification) tabulated in a PTMTAB file. I have several issues with this file. Foremost, I am not ...
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1 vote
0 answers
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Database of predicted protein-ligand binding/docking score

Is there a database of computationally determined "binding scores" across protein-ligand pairs in the PDB? My phrase "binding score" is deliberately generic, since any such score would be fine. In ...
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3 votes
2 answers
631 views

What direction is a sequence in databases written?

In many databases, the DNA sequences for proteins are given as a string of a,t,g,c without specifying whether the starting is from 5' or from 3'. Also it is not specified if it is the coding or non ...
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