Questions pertaining to organized collections of biological data.

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3
votes
2answers
43 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 ...
2
votes
1answer
54 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 ...
0
votes
1answer
76 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?
6
votes
0answers
233 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 ...
3
votes
0answers
54 views

Database of Medical Assertions

Can anyone point me toward a computationally-accessible database of medical assertions? I'm looking for something where each row in the database contains a single unit of knowledge. It could either be ...
2
votes
0answers
123 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
0answers
70 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 ftp://ftp.ncbi....
2
votes
0answers
31 views

Is there a database of pollen-seed distances across plant species?

I was enjoying Richard Smith's excellent answer to this question, and wondered: If you consider the pollen/seed distribution range to be plant locomotion, is there a database that compares these ...
1
vote
0answers
39 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 ...
1
vote
0answers
55 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 ...
1
vote
0answers
31 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
0answers
36 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 ...
1
vote
0answers
24 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?
0
votes
0answers
12 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
0answers
272 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 ...