Questions tagged [database]

Questions pertaining to organized collections of biological data.

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2
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0answers
24 views

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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1answer
589 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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30 views

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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7 views

Regalecus glesne or Regalecus russelii?

I was doing research on Regalecidae, and I came across an online database. Here, on the database, there are 12 matches for Regalecus russelii. At the bottom of most of these pages, there is a related ...
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36 views

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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5 views

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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46 views

Where can I find anthropometric data for different ethnicities?

I get that this is a sensitive topic, but please trust me, the very reason I'm asking is because I want to represent a people properly. There's a video game where peoples of different ethnic ...
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21 views

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...
4
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2answers
436 views

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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1answer
13 views

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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25 views

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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3answers
165 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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1answer
59 views

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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1answer
28 views

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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1answer
73 views

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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11 views

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 ...
3
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1answer
25 views

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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1answer
33 views

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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15 views

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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21 views

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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41 views

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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1answer
34 views

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 ...
3
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1answer
117 views

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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0answers
155 views

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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3answers
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-...
5
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1answer
572 views

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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1answer
114 views

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 ...
2
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1answer
55 views

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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1answer
63 views

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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0answers
48 views

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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1answer
39 views

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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2answers
50 views

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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2answers
119 views

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 ...
5
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2answers
230 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 ...
1
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1answer
93 views

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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1answer
33 views

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 ...
3
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0answers
37 views

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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0answers
23 views

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 ...
3
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2answers
467 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 ...
3
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0answers
49 views

How much Open Access Data is there in genetics? [closed]

Type of data of interest I would like to consider Genetics data (SNP, microsatelites, whole genome sequencing, RFLP, ...) Genetic - phenotype data (disease-related data, QTL, etc...) Sequence ...
2
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2answers
456 views

How to search NCBI in bulk for a list of accession numbers?

I have a large ( >100 ) list of accession numbers I want to look up and match to searches in NCBI (nucleotide); mainly for getting a tentative organism to match to the accession number. ex: ...
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0answers
20 views

Which scientific names designate eyespots?

I've found that names containing ocellata‎ and ocellatus‎ designate species that feature eyespots. Are there other words in the scientific names that designate eyespots? The problem I need to solve ...
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0answers
341 views

Specific activity vs turnover number of enzymes in BRENDA

From my understanding, the specific activity (A, units: umol/min/mg protein) can be derived from the turnover number (k, units: 1/seg) and the molar mass of an enzyme (MW, units: g/mol): A = k / MW / ...
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0answers
44 views

What's the best source characterizing proteolysis cleavage sites in the phagolysosome?

I have found MEROPS and TopFIND via the survey paper Quantitative proteomics and terminomics to elucidate the role of ubiquitination and proteolysis in adaptive immunity. These look like a good start, ...
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0answers
40 views

Do GPCRs have 7TMHs?

I've screened a non-redundant set of GPCRs acquired from UniProt. I found a handful of examples of record IDs that contain more than the 7 TMHs. For example Q89609 and P20905, both of which have been ...
2
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1answer
1k views

What is the length of gene when calculating TPM (transcripts per million)

What is the length of gene when calculating TPM (transcripts per million)? Assume I have a dataset matrix with k rows(each row is a gene) and n columns (each column is a sample), is there any way I ...
0
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1answer
30 views

Is there a database for immunoglobulin domain structure?

is there a database where I can find the sequences of the hypervariable domain of immunoglobulins and the sequences of the related antigens? Thank you
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2answers
72 views

Analyzing Messy Data Files [closed]

I was writing some code scripts to analyze some plasmodium spp. using this database. However the names assigned to the various epitopes and other items on the list is very very very disorganized. In ...
2
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0answers
125 views

Protein/ligand affinity databases?

Is there any database that contain binding affinities reported in litterature for different proteins and ligands? I have checked uniprot already and it does not seem to included any binding affinity ...
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0answers
33 views

Get Network Out of proteins of interest

I have generated a list of Proteins using oncogeenes and suppressor genes of cancer. I have 5827 mapping identifier for 3916 interactions using STRINGdb R package . How do I build a network of 200k ...