Questions tagged [database]

A repository for data that is organised according to specific rules. Important biological databases include PDB (Protein Data Bank), Ensembl, Uniprot.

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Where to download JASPAR TFBS motif bed file?

I am interested in determining if any transcription factor binding site motifs are enriched in some BED files from a DNA methylation experiment. I am looking for a database that has BED Files ...
Reilstein's user avatar
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19 votes
6 answers

Are there any RepBase alternatives for genome-wide repeat element annotations?

I’m using the RepBase libraries in conjunction with RepeatMasker to get genome-wide repeat element annotations, in particular for transposable elements. This works well enough, and seems to be the de ...
Konrad Rudolph's user avatar
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
13 votes
6 answers

Converting gene names from one public database format to another

This is a question from /u/apivan19 on reddit. The original post can be found here. I have some proteomics data that was given to me with the UniProt gene identifiers in column 1. I've been trying to ...
gringer's user avatar
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13 votes
6 answers

Are there any databases of templates for common bioinformatic file formats?

I want some templates of different file formats that I can use to test my scripts and identify possible bugs in my code. For example, consider nucleotide FASTA, a simple but often abused format, I ...
Chris_Rands's user avatar
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9 votes
2 answers

How to import a large amount of .bed, .gff, .vcf, .paf, .sam files into an SQL database?

Are there best practices to load different bioinformatics file formats such as VCF, BED, GFF, and SAM to SQL databases? I am wondering how people out there do that efficiently. All of these three ...
0x90's user avatar
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7 votes
6 answers

How to get a list of genes corresponding to the list of SNPs (rs ids)?

Is there a way for me to get a list of genes given a list of SNP rs ids? I found several questions asked with a similar goal years ago, and the answers are always about using multiple online tools, ...
Haohan Wang's user avatar
4 votes
1 answer

Extracting a cytochrome B sequence from NCBI's nucleotide database

Can someone tell the way to extract the fasta sequences for the gene cytb of Acetes japonicus (shrimp important to China and South Korea)? Can I extract them directly from NCBI nucleotide database (i....
Sofia's user avatar
  • 351
4 votes
1 answer

Duplicate gene symbol handling in GEO gene expression data

I have downloaded a gene expression data from GEO database (GSE3268) in which in some of its rows there are duplicate gene symbols. For example TP53 exists in two rows with different expression values ...
Majid's user avatar
  • 143
3 votes
2 answers

How can I find mutations associated with disease in human histone residues?

I would like to look if there are mutations in residues of human histones associated with any disease. For instance, if a mutation in residue K6 (lysine 6) of histone H2A1A is associated with any ...
plat's user avatar
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0 votes
1 answer

Use of Electronic Phenotype in EHR

May I know what's the use of Electronic Phenotyping using EHR data? I did refer this link but have few questions I understand that ...
The Great's user avatar
  • 217