Questions pertaining to organized collections of biological data.

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6
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1answer
159 views

Is there a karyotype database for human cell lines?

I'm looking for the karyotype of a specific cell line. Some karyotype are well known, such as HeLa or some carcinomas, but some are very hard to find, such as LG2 (B cells). Is there a database ...
0
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0answers
11 views

Do you know of any scratch assay video databases?

It would be of great help for a statistical work we have been asked to carry out at our University. Thank you very much in advance.
0
votes
1answer
16 views

what is the principle behind Allele Frequency Net Database

I just wanted to know what is the basic principle of Allele*Frequency Net Database. How are the frequencies present in them calculated??
0
votes
1answer
31 views

How can I find the most studied SNP of a gene?

How can I find the most studied SNP of a gene and diseases that the most studied SNP has been related to? I search in dbSNP database but I can't find it. What is the process?
1
vote
1answer
47 views

how to change format of ent file into PDB format?

whenever i download files from Protein Data Bank(PDB),they are downloaded in .ent format. How can i convert them into PDB format??
12
votes
3answers
135 views

Where can I find historical data on world-wide ecology parameters?

I hope this is the right StackExchange forum for such a question. I'm looking for large data sets on world-wide ecology parameters, such as annual temperatures by latitude, annual rainfall, CO₂ and ...
1
vote
1answer
53 views

open database of medical images

Does anyone know of an open repository of medical images (e.g., CT scans) organized by disease category? I'm working on some computer vision software that requires a large set of controls from which ...
4
votes
3answers
69 views

Where can you find the quantities of each amino acid of a particular protein or food?

Taking a potato as an example. If I wanted to know how much µg or % of each of it's amino acids there are in 1 gram of pure potato protein, where can I find this information? Is there a freely ...
3
votes
3answers
36 views

Is there a database providing information about optimum temperature and inactive temperature of enzymes?

I want to know optimum and inactive temperature of some enzyme, but I can't find these information in NCBI, wiki or UniProt. So I want to know if there are some database which provide these ...
0
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1answer
28 views

Why does uniprot sometimes not label single-pass transmembrane proteins as “anchors”?

Currently, section 3a) of unitprot TRANSMEM reference page divides single-pass transmembrane proteins into 4 types: ...
5
votes
2answers
151 views

Where can I find mutation datasets for cancer?

My lab has been using TCGA data (somatic mutations and clinical data) to develop panels of genes and of mutations we expect to see in certain cancer populations. We'd like to validate our panels by ...
0
votes
1answer
40 views

What does uniprot consider “unambiguous” evidence for the subcellular domain of a protein?

Uniprot has annotation for subcellular location of protein domains. This topological domain information of proteins is under the TOPO_DOM flag. In most cases the ...
1
vote
0answers
46 views

How to find name of the gene

Considering the kegg page, this page contains the description of the gene Edwardsiella tarda EIB202: ETAE_0074 . Now this gene has a name given in the page as : wabG. Now considering another gene 1 ...
3
votes
2answers
41 views

Is there a web tool for species identification?

I know this stack exchange provides the ability to post photographs of animals/plants for species identification, but is there a web resource that can automatically identify a plant/animal using image ...
3
votes
2answers
117 views

Is there a database of cell images?

We're working on an algorithm for processing images of cells, similar to but much more basic than Cell Profiler, and we are looking for a large database of cell images to test our software. Can anyone ...
1
vote
0answers
28 views

Genotype-Phenotype databases?

Beyond the Stanford HIV database, what other databases out there provide a dataset linking virus/bacterial genotype to quantitative phenotype? I'm looking for high quality datasets to test machine ...
1
vote
1answer
55 views

Human population growth - where can I find the data?

Out of curiosity, I'd like play around with data of human global demography. Where can I find data that describe the "per region (per continent for example) population size" versus time since the ...
13
votes
2answers
988 views

Why and how does uniprot list around 150,000 proteins in the human genome?

Using organism:"Homo sapiens (Human) [9606]" as a query in uniprot returns about 146,000 proteins. I was under the impression that there were only 20-25,000 protein ...
0
votes
0answers
134 views

Online Database for PPG (Photoplethysmography) signals (both Infrared and Red light readings)

I am looking for an online Database for PPG (Photoplethysmography) signals for SPO2 (oximetry) analysis. I have tried several sources but they only have single datasets labelled "PLETH" and not ...
2
votes
2answers
59 views

Database of medically validated SNPs

I'm looking for all possible sources of clinically tested human SNPs. There is a handful of databases that store SNPs (like dbSNP), but I only need those that have validated presence/absence of ...
0
votes
1answer
31 views

Finding a reaction from a KEGG map

I have come across a map and a part of it looks like this: Now I have not been able to locate the reaction that converts alpha D-Glucose to Glucono-1,5-lactone but was successfully able to locate ...
7
votes
1answer
134 views

Database of Geographic Range of Species

Is there a database of organisms which would contain their queriable geographic location? I would need to perform a rather simple query, such as ...
4
votes
1answer
166 views

What do “e” “-” “C” and “E” mean in this output?

I have given an input of this protein sequence: MEPVDPRLEPWKHPGSQPKTACTTCYCKKCCFHCQVCFTTKALGISYGRKKRRQRRRPPQGSQTHQVSLSKQPTSQPRGDPTGPKE from this website along ...
2
votes
1answer
37 views

Why is there a compound highlighted in red in a KEGG Module search?

Considering the following module: http://www.kegg.jp/kegg-bin/show_module?M00115+C00003 why is the compound C00003 marked in red?
0
votes
1answer
30 views

Presence of reaction module in bacteria but not in Eukaryotas (human)

From the statistics page, I found that the Module-M00008 is present only in bacteria and not Eukaryotes. Why so? I noticed that all the compounds necessary or the reaction are present in human body ...
1
vote
1answer
18 views

What information does the KEGG Module statistics page show?

While browsing through the home page of KEGG Module, I clicked the button named Module statistics. Can someone tell me what does these numbers signify? What are they the statistics of?
1
vote
2answers
73 views

Difference between modules in KEGG Module

The KEGG module M00115 includes a set of reactions while M00542 does not have any; it just shows the list of enzymes. Is the reaction set for M00542 still unknown?
0
votes
1answer
38 views

How reliable is SwissProt topology?

I am using TOPO_DOM annotations from uniprot databases to characterise the orientation of transmembrane features. Is SwissProt topology experimentally validated, ...
4
votes
0answers
82 views

How to gather life-history traits data on bird species?

I am looking for a data base of life history traits for bird species. Is there such data base? If not, what are your advice on how to collect those data? Is there a handy website that list ...
1
vote
1answer
24 views

Any databases with AAMI ECG and ECHO?

There is no AAMI 12-lead ECG databases available online. All of them have problems. I and my friends finally finalised our tests with St Petersburg. It is not AAMI. So the next step is to search ...
-3
votes
1answer
60 views

From where can I download the database created by Hsu et al for MORFs? [closed]

I am working on an independent research project for which I require access to the MORF database created by Hsu et al. From where can I download the database of MORFs of IDPs and their binding partners ...
4
votes
1answer
63 views

How to seek for available genetic data relevant to ecology and evolution?

I had a quick look online. There seems to exist many different website of database archiving. Some data might be free of charge while some others might not be. I found things such as Dryad, TreeBase, ...
5
votes
1answer
68 views

Calling for Free Online Data for Paediatric ECG?

I need free online data about heart murmurs to study these: heart murmur frequency , S2 heart sound frequency and its split, murmur timing, and duration, murmur intensity, S3 sound presence and ...
0
votes
1answer
76 views

Finding Rna-Seq dataset for C. Elegans (Caenorhabditis elegans)

I want to find a RNA-Seq dataset for C. Elegans to use it in RNA-Skim software. For those who does not know RNA-Skim let me explain it a bit. It is a tool which is used to quantify RNA-Seq data using ...
3
votes
1answer
76 views

Resources of all known biochemical pathways?

I am looking for a encyclopedia or biochemical pathway atlas of all known or reported pathways. I am very much interested in network and systems biology. Also the references can be open databases, ...
3
votes
1answer
168 views

What is the difference between “physical interaction” and “genetic interaction”?

I searched sac1 in uniprot to know more about this gene. in interaction I selected this link and there I see that this gene has some "physical interactions" and "genetic interactions". I am wondering ...
0
votes
2answers
108 views

Difficulties understanding a pathway [closed]

I am not a biologist and I would love to understand what is going on with this pathway. I went to the description but it's still complicated, and I couldn't follow. Can someone please help me with it? ...
2
votes
0answers
102 views

Is there a database of known riboswitches?

I'm looking for sequences and annotations of known riboswitches, but so far I haven't found a resource that actually fulfills my requirements. The best database I found so far is Rfam, which has ...
2
votes
2answers
103 views

Downloading specific yeast genes in an automated manner?

I have 6 genes of Candida albicans yeast namely orf19.723, orf19.5908, orf19.610, ...
1
vote
0answers
34 views

Download FunCat Database for Programmatic Access

I am enriching RNA-seq data for the fungus Neurospora crassa and would like to be able to search the genome by functional category, determine similarity of genes by category membership, and any other ...
6
votes
1answer
61 views

How to search for organisms by criteria such as growth substrate and overflow metabolites?

I'm looking for a database or a systematic way to search for organisms which meet certain criteria. My criteria descending importance are: growth substrate chemolithoautotrophy (on which substrate) ...
2
votes
3answers
145 views

Is there an online gene library? [closed]

Is there an online library that includes all known genes in stored in their nucleotide form of all living organisms? Note I am not necessarily looking for a human only database. If such a database ...
0
votes
2answers
37 views

Resource for finding what proteins bind?

I have two lists of proteins (including phosphorylated forms). I want to determine which members of each list act on which members of the other list. What online resources exist for finding out what a ...
1
vote
0answers
21 views

Recombination frequency as a function of genomic location in E coli?

Are there any databases or papers that give recombination frequency as a function of position in the E coli genome?
1
vote
2answers
370 views

What are the rules for plasmid names?

What are best practices for naming newly created plasmids? For example, a common format is pABC123. What is the exact specification? Must there be 3 letters? What ...
1
vote
1answer
40 views

programmatic fast search of 100-1000 short reads to a public server and obtain list of nearby genes

What are the options for programmatic fast searching of 100-1000 short reads to a public server and obtain list of nearby genes where the reads map? Input: ~100-1000 short reads Output: GFF list of ...
1
vote
1answer
90 views

Dataset of microscopic images before and after staining?

I am looking for a freely distributed dataset of microscopic images. I am hoping to find a dataset that would feature histological images before and after staining (e.g. H&E or some other standard ...
4
votes
2answers
161 views

Database of Multicellular and Unicellular organisms?

I'm trying to annotate a list of organisms taken from NCBI for cellularity (unicellular or multicellular). Does any of you ever found a database with association between an organisms' name or taxa and ...
2
votes
0answers
54 views

dbSNP database table desciptions

I am trying to build a local implementation of dbSNP. I would like to know the descriptions of tables listed on ftp://ftp.ncbi.nlm.nih.gov/snp/database/organism_data/human_9606 and on ...
5
votes
1answer
275 views

Local storage of NCBI database in MongoDB [closed]

My short term goal in a project is to build a local database of the NCBI dbSNP database. The data and schema are available on the FTP site(). I was going to implement the database using MySQL, but I ...