Questions tagged [public-databases]

Use this tag for questions about how to use, download, retrieve, check and browse public databases.

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5 votes
3 answers

How to determine the primary Uniprot accession number from a set of accession numbers?

Given a list of Uniprot IDs that are linked to an Ensembl gene ID, is there a way to systematically determine the UniProt accession corresponding to the protein product of the gene's primary ...
James Draper's user avatar
4 votes
1 answer

Missing data mappings in while trying to convert Genes Ensembl Ids to Entrez Ids

I need to convert a lot of Ensembl Ids to the relative counterpart in Entrez (e.g., ENSG00000157764 > 673). I found ...
floatingpurr's user avatar
5 votes
2 answers

How can I work out gram staining information from the species name?

I have a very long list of prokaryote organism names. I would like to know their gram staining (gram positive or gram negative) information. Please let me know if there is any database that keeps ...
Arijit Panda's user avatar
3 votes
1 answer

Database of copy number alterations in different cancer types

Is there a database of somatic copy number alterations (CNAs) in different cancer types? That is, annotations of which CNAs are more commonly seen in different cancer types.
719016's user avatar
  • 2,324
7 votes
1 answer

Where can I find summary data for how common certain mutation *types* are?

I'd like to know how common certain mutation types are in public data sets like the 1000 Genomes, ExAC, and ESP6500. Specifically, I'd like to know the distribution of stop-gains, stop-losses, ...
Mark Ebbert's user avatar
  • 1,304
6 votes
3 answers

Secretome and membrane receptor profiles

I am looking the secretome profile and the membrane receptor profile for a given cell type. In my specific case, this should be the secretome and outer membrane receptor profiles of dorsal root ...
jaslibra's user avatar
  • 524
4 votes
1 answer

Get canonical transcript from UCSC

I am using the following command to get all refseq genes from UCSC: ...
terdon's user avatar
  • 9,662
-1 votes
1 answer

Bioperl - how can i print first result of search sequence per iteration?

MTG's user avatar
  • 147
2 votes
1 answer

Is Wikidata a reliable KB for genomic and drugs annotations?

I'm looking for a Linked Open Data approach to annotate a dataset with human genome and drugs information. According to the Linked Open Data cloud, there are a lot of interconnected ...
floatingpurr's user avatar
14 votes
3 answers

How to obtain .bed file with coordinates of all genes

I want to get a .bed file with the genes' names and canonical coordinates, also I would like to have coordinates of exons, too. I can get the list from UCSC, however, if I choose UCSC Genes - ...
German Demidov's user avatar
7 votes
1 answer

What is a good pipeline for using public domain exomes as controls?

I'm currently attempting association analysis with an extremely small set of patient exomes (n=10), with no control or parental exomes available. Downloading the ExAC VCF of variant sites (http://exac....
carsweshau's user avatar
6 votes
2 answers

How to select a cutoff for interaction confidence in STRINGdb?

I have a list of 100 genes that are called as hits in a genetic screening. I want to have a network of the interactions between the proteins of these 100 genes. I am using both STRINGdb web and its R ...
plat's user avatar
  • 1,022
15 votes
3 answers

Publicly available genome sequence database for viruses?

As a small introductory project, I want to compare genome sequences of different strains of influenza virus. What are the publicly available databases of influenza virus gene/genome sequences?
AlwaysTrying44's user avatar
11 votes
3 answers

How to extract RNA sequence and secondary structure restrains from a PDB file

I'm trying to find a programmatic way to automatically extract the following information from a PDB file: RNA sequence Secondary structure restraints in bracket format, e.g. ...
Peter's user avatar
  • 343
6 votes
1 answer

Entrez or Ensembl gene IDs?

I'm using several datasets that are encoded using either Entrez or Ensembl IDs to specify genes, and need to decide on which to standardise on. Are there any major reasons to use one over the other? ...
user avatar
13 votes
3 answers

Given a VCF of a human genome, how do I assess the quality against known SNVs?

I'm looking for tools to check the quality of a VCF I have of a human genome. I would like to check the VCF against publicly known variants across other human genomes, e.g. how many SNPs are already ...
ShanZhengYang's user avatar

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