Questions tagged [database]

Questions pertaining to organized collections of biological data.

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2
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2answers
496 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
354 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, ...
2
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0answers
43 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
2k 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 ...
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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
1
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2answers
75 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
127 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
35 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 ...
2
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0answers
64 views

String-db locally downloaded

I need a ppi network of cancer and it should have 200k to 300k proteins (nodes) As the web inteface don't allow more than 2000 ...
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1answer
152 views

Stringdb using R Bioconductor package

I need to retreive a large dataset from String-db. I 'm newbie in R so even with the documentation , I could not get the dataset fron String How do I do to retreive a network from String 2k to 3k ...
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0answers
51 views

Biogrid interaction protein network

I need a ppi network for cancer or Alzheimer . I'm using BioGrid , In the search field I can specify the gene id only , I want to know how can I make an interaction network for one of the disease ? ...
0
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1answer
40 views

Retrieve the associated annotation from Uniprot

I have a dataset that I extracted using Cytoscape and STRINGAPI Hoz can I retreive the annotation of that network from uniprot as it has more than 1k proteins . and doing it manually is not possible
6
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1answer
263 views

Where can I find large datasets of protein-interaction networks?

Where do I find large datasets of protein interaction networks for cancer or alzheimer diseases? So far, I found String but it is does not have enough proteins for my purposes. Are there such ...
7
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3answers
104 views

Global database for patients with rare and important injuries or disease?

I was recently reading Christof Koch's The Quest for Consciousness, and several times he mentioned how important some patients with sad and terrible brain injuries were for the understanding of the ...
6
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1answer
2k views

How many proteins are in the Earth's proteome? [closed]

Humans alone have thousands of proteins. With that in mind, it seems like the total number of proteins among all species would be very large. Are there any available estimates for how many proteins ...
2
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0answers
56 views

Open access datasets for QTL analysis?

I'm just getting started out learning how to use the QTL package in R studio, and I'm trying to find additional datasets to practice with. I've already worked through the datasets here on the Rqtl ...
7
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1answer
73 views

Where can I find comprehensive data on animal distribution?

I'm looking for vertical distribution or tidal height of several intertidal species, specifically from the Pacific Northwest. I considered looking for published research for each species however, my ...
2
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1answer
957 views

Meaning of ‘NC number’ associated with a gene?‘

Genes in listings etc. often have a number of the type NC_000012.12 associated with them. How should this be interpreted?
4
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2answers
95 views

Looking for a database of plant features

To perform some private data science experiments I am looking for accessible information on morphological plant features (tabular information would be best). Crawling the web I found many websites ...
4
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1answer
584 views

Database for drug-target relation

I'm writing a thesis on bioinformatics and looking for drug-target databases. I'm implementing a open-source application for a tool called Cytoscape and so far I've used a open-source database called ...
5
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1answer
103 views

Database of cancer cells

I am looking for a database(or any kind of information source) of cancer cells, which has information about the speed of reproduction of these cells, how fast they grow, etc. So I could make my ...
2
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0answers
86 views

Database of time lapse stem cell differentiation

Currently I am working on a project about modelling the social behaviours of embryonic stem cells (or induced pluripotent stem cells). I need a series of time-lapse live cell images which recording ...
3
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1answer
56 views

How to automatically obtain the “kingdom” of a species from its name?

I'm looking for a simple way (such as a database) so that a program can get the kingdom of a species, knowing its name (such as "Prunus persica"). As a matter of fact the species I'm concerned with ...
8
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1answer
165 views

What is the most-stable gene identifier?

I've struggled in the past with designing data(bases) around gene-identifiers that evolve over time. For example, UniProt and Ensembl change their identifiers for certain proteins/genes and the IDs ...
12
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2answers
3k views

Online phylogenetic tree of human lineages

I am looking for a source of information about the diversity of human lineages and their relationships. With a quick google search it is easy to find this type of tree A perfect online resource ...
2
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0answers
711 views

Drugs with unknown mechanism of action

I want to get a list of FDA-approved drugs with unknown mechanism of action. I think that there should be a database where for each drug there is a short field "mechanism", but I haven't find one. Do ...
2
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1answer
182 views

databases for plant growth temperature and altitude

Does anyone know databases which have info for plant growth temperature.It could be specific numbers or categorization as 'cold, warm,tropical and etc' ?
14
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4answers
3k views

Where can I get a file/list of the common and scientific names of species?

I am searching for an un-encoded data file with common and scientific names for example of a few hundred species or tens of thousands, where I can search the common and scientific labels of organisms.
8
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2answers
2k views

The best free and most up to date phylogenetic tree on the internet?

I found phylogenetic tree in wikipedia is lacks of accuracy. It actually confusing with versions. Some terms was not scientifically accurate with dna analysis anymore So are there anyone know where ...
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0answers
33 views

Difference between curated publications and additional publications in nextProt database?

With reference to reference papers listed in nextProt database, what is the difference between curated publications and additional publications? Anyone using nextProt, kindly explain the terms. For ...
2
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1answer
31 views

Availability of a database containing the proteins of Vibrio cholerae and their corresponding gene sequences

I wanted a list of all the proteins (amino acid sequences) and their corresponding gene sequences of Vibrio cholerae. I tried to search in patric, but the number of amino acid sequences and gene ...
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2answers
3k views

What does curated gene mean? [closed]

I see in databases "curated" or "not curated" for genes. What does that mean?
3
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1answer
81 views

This Sequence Data (DNA) has very few Methionin-starts. How is that possible?

I'm working on my first sequencing related project and I'm trying to find proteins with a specific PFAM ID (PF11999). The project is called "MMETSP", I searched the annotations for that ID, identified ...
3
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4answers
127 views

How do I effectively visualize data showing change in a lot of samples over two time periods? [closed]

I've tallied the number of glands in a plant this year and last year. My full data set has about 20 plants in it (I've reproduced the data from 10 of the plants here). I want to show that the plants ...
3
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2answers
3k views

How to batch convert gene names to protein IDs in Uniprot?

I have a list of >1000 "ordered locus names" from the STRING database (also called gene numbers, ORF numbers, or CDS numbers by uniprot). They're in the form of 'b0014', 'b0015', etc. I'd like to ...
1
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1answer
545 views

ExAC Browser: What does a “dubious variant annotation” mean? [closed]

I am studying a protein in the ExAC browser. However it is flagged with a "LoF flag". What exactly counts as a "dubious" variant in ExAC. I couldn't find any further information neither at the ...
1
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1answer
141 views

4DGenome or another comprehensive database of chromatin interactions

I'm searching for the most comprehensive source of chromatin interactions to support enhancer targets (data such like Hi-C, ChIA-PET, IM-PET, 5C, 4C, 3C, etc.) and my question according that could be ...
1
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1answer
104 views

Distribution of Exon and Intron Sizes

Goal I am trying to get a distribution of Exons and intron sizes in Three-Spined Stickleback (Gasterosteus aculeatus). Data downloaded I downloaded some data from Ensembl. More precisely, I went ...
2
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1answer
146 views

How to retrieve logical expression (KO based) for reactions from KEGG?

Whether a module is complete or not can easily be checked by evaluating the Definition entry associated with the module; e.g. in module M00010, it is given by <...
2
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2answers
1k views

How to find PDB id of an amino acid sequence

Suppose I have an amino acid sequence whose PDB id is unknown. Is there in online server that can find the PDB id of the corresponding amino acid sequence? is there any site that will find the pdb ...
2
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2answers
641 views

Coordinates of amino acids in a protein sequence

In PDB format, the coordinates of each of the atoms are available. Are the coordinates for the amino acids available separately? As in say a protein sequence consisting of a chain of amino acids MKL......
1
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1answer
161 views

Data on Recombination rate and Gene Positions in Humans

I am looking for estimates of per base pair recombination rate in humans and indication on gene positions. The goal is to be a able to plot recombination rate in the y-axis and position (in bp) along ...
3
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1answer
125 views

How do I retrieve electronic annotation from Uniprot and GO records that relates to molecular function?

I'm interested in the endonuclease activity of the G3BP1 gene, specifically the uniprot record Q13283. An external link guides me to UniprotKB-KW electronic annotation. How can I retrieve valuable ...
4
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2answers
257 views

Grouping OMIM disease codes

I have ~100 sets of genes, and each set includes between 2 and 70 genes. I'd like to perform an enrichment analysis on each of these sets to test if they're enriched for OMIM disease labels. However, ...
5
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2answers
502 views

How to obtain a list of proteins sorted by the ~1400 unique protein folds?

The databases CATH and SCOP both have around 1400 unique protein folds recorded from analysis of the PDB. However, I do not see any method to access this particular data. A list of each of the 1400 ...
7
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1answer
195 views

How can I make a protein interaction/protein-complex network?

Let's say I have a list of proteins ID. I would like to know whether I can find any complex based on that list. Any example, explanation is appreciated. An example input is what you see below. What ...
3
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1answer
213 views

Understanding common identifier codes (IDs) in biology databases

I know this is very basic but I would like to understand it and it's difficult to know where to begin with a new database. I have the output: ...
2
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2answers
103 views

Protein-protein interactions search

I used STRING db in order to find all the interactions of the precursor protein APP. What I specifically need is a confirmation (supported by some article and experiments in it). But significant ...