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Questions tagged [database]

Questions pertaining to organized collections of biological data.

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KEGG map01100: Is this ectomycorrhizae or arbuscular mycorrhizae

Just as background mycorrhizae are fungi and split into two groups ectomycorrhizae and arbuscular mycorrhizae (AM). Taxonomically these fungi groups are very distinct. Ectomycorrhizae belong to the ...
M__'s user avatar
  • 159
0 votes
1 answer
46 views

Is there a comprehensive Taxonomical ID database?

I know there are resources that outline the latest taxa, such as wikispecies or Kew Gardens. However, I have not found any resources which detail the defining features of each taxa. Are there any ...
imrobert's user avatar
  • 450
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0 answers
18 views

Databases medicine and therapy - animal & human studies, technology readiness level

I am looking for some universal databases that would offer information about drugs and therapies currently in development. The area of interest is mostly cell and gene therapy. I am looking for ...
menshiki's user avatar
0 votes
0 answers
16 views

Estimation of carbon stock value

I would like to ask, to calculate the carbon value estimation, the Allometric formula is of course used, but in some of the literature I searched, I found different allometric formulas but the same ...
ana's user avatar
  • 1
0 votes
0 answers
29 views

Database of insect sounds

I was thinking last night as I laid listening to the loud insects at night here in Georgia, that I wanted to be able to hear the bug sounds people listen to all over the world. Could not find much ...
Jonathan's user avatar
3 votes
1 answer
37 views

Database for commercially available restriction enzymes?

I need a database that contains a complete list of commercial restriction enzymes: name of the enzyme & recognition site.
Freezing Soul's user avatar
1 vote
1 answer
33 views

Is there a database for fossilized coral reefs that have been reported?

Given that coral lives only up to 5,000 years, and I assume marine biologists have maps of where all known living reefs are around the world for research and monitoring, where can I find information ...
SeligkeitIstInGott's user avatar
0 votes
0 answers
236 views

Is there a dataset for the optimum conditions (Temperature, humidity, light intensity, etc.) for plants growth?

I'm a student working on an automated greenhouse. I wanted to add a database for the most commonly grown plants and the optimum conditions needed (I'm mainly looking for temperature, humidity, and ...
Belal Bahaa's user avatar
1 vote
2 answers
56 views

Accessing the recombination map of Drosophila melanogaster

I'm looking for some information on the data of a recombination map of Drosophila melanogaster. In 2012, an extensive study by Comeron et al. appeared saying that they had reconstructed a ...
arara's user avatar
  • 696
1 vote
1 answer
107 views

What are the W and DSM codes for the following bacteria referring to?

In this paper the following bacteria are listed: Bifidobacterium bifidum W23 (DSM 26331) Lactobacillus salivarius W24 (DSM 26403) Lactobacillus acidophilus W37 (DSM 26412) Lactobacillus casei W56 (...
Rob Simpson's user avatar
2 votes
0 answers
8 views

database of Animals/insects which would contain their queriable geographic location?

Is there a database of Animals/insects which would contain their queriable geographic location? I would need to perform a rather simple query, such as ...
S.Safire's user avatar
2 votes
0 answers
29 views

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 ...
Dermot Harnett's user avatar
0 votes
2 answers
78 views

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 ...
micoay's user avatar
  • 11
0 votes
1 answer
233 views

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 ...
Yuri Rolimus's user avatar
0 votes
1 answer
84 views

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 ...
qqqqqqq's user avatar
  • 111
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1 answer
63 views

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-...
ceno980's user avatar
  • 1,741
2 votes
0 answers
47 views

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 ...
cavalist's user avatar
1 vote
1 answer
33 views

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 ...
ceno980's user avatar
  • 1,741
-4 votes
1 answer
55 views

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 ...
Chris's user avatar
  • 35
0 votes
1 answer
24 views

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 ...
drew.neely's user avatar
3 votes
0 answers
43 views

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? ...
Lance's user avatar
  • 759
2 votes
1 answer
27 views

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 ...
E Tam's user avatar
  • 852
0 votes
0 answers
18 views

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, ...
Robrecht's user avatar
2 votes
0 answers
30 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 ...
gk582lf582s's user avatar
3 votes
1 answer
1k 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?
gk582lf582s's user avatar
4 votes
0 answers
31 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 ...
Owen's user avatar
  • 41
0 votes
0 answers
117 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, ...
Toke Faurby's user avatar
1 vote
0 answers
12 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....
Gabs's user avatar
  • 111
0 votes
0 answers
26 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...
Shale's user avatar
  • 101
5 votes
1 answer
491 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 ...
Steve Crawford's user avatar
1 vote
1 answer
53 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 ...
himanshu saraswat's user avatar
1 vote
2 answers
464 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 ...
lolmaus - Andrey Mikhaylov's user avatar
0 votes
3 answers
261 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 ...
Galen's user avatar
  • 1,045
-1 votes
1 answer
74 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 ...
Andy Ljunggren's user avatar
1 vote
1 answer
34 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 ...
girl101's user avatar
  • 2,215
0 votes
1 answer
153 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. ...
Grant Hartlage's user avatar
1 vote
0 answers
17 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 ...
RAHenriksen's user avatar
3 votes
1 answer
39 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 ...
mercury0114's user avatar
0 votes
1 answer
35 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 ...
Мікалас Кaрыбутоў's user avatar
0 votes
0 answers
18 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 ...
JonJup's user avatar
  • 31
0 votes
0 answers
45 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 ...
Lokasa Mawati's user avatar
0 votes
0 answers
70 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, ...
User's user avatar
  • 143
1 vote
1 answer
56 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 ...
User's user avatar
  • 143
3 votes
1 answer
157 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 ...
Joey Gough's user avatar
1 vote
0 answers
237 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 ...
AL B's user avatar
  • 111
18 votes
3 answers
3k 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-...
Jared's user avatar
  • 289
5 votes
1 answer
799 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 ...
WoJ's user avatar
  • 525
1 vote
1 answer
128 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 ...
Lance's user avatar
  • 759
2 votes
1 answer
89 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 ...
Lance's user avatar
  • 759
0 votes
1 answer
92 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, ...
FIREREED's user avatar