Bioinformatics Research Guide: Genomics - Databases

The Kyoto Encyclopedia of Genes and Genomics (KEGG) is a massive database of genetic information from a vast array of organisms covering members of Animalia, Plantae, Fungi, Proista, Archaea, and Bacteria. The site contains information on biochemical pathways, gene orthologs between species, gene products, species proteomics, small molecule compounds, enzymes, post-translational modification, human disease, and drugs.

Link: https://www.genome.jp/kegg/

Operating Institution: Kanehisa Laboratories

Supporting Institution(s): National Bioscience Database Center, Institute for Chemical Research - Kyoto University

 

The UCSC Genome Browser is a collection of genetic information for a wide array of vertebrate model organisms. The database allows for the alignment of gene sequences for analysis, visualization of genetic data, perform PCR primer analysis, and production of phylogenetic trees. 

Link: https://genome.ucsc.edu/index.html

Operating Institution: University of California at Santa Cruz - Genomics Institute  

Tutorials: 

YouTube Channels - Multitude of tutorial videos 

FAQ Page

User Guide - Documents on how to use the database

GenomeWiki - Wiki style site that contains information on how to use the site and other community features 

GWASdb is a database of various genetic variations found to be associated with disease states identified through genome wide association studies. The database provides following functions:
(i) In addition to all the TASs attained genome-wide significance (P-value < 5 x 10^-8), we manually curated the TASs that are marginally significant (P-value < 10^-3) by looking into the supplementary materials of each original publication;
(ii) Extensive functional annotations and predictions for those TASs across multiple domains;
(iii) Furthermore, we have manually mapped those TASs by phenotype according to Disease Ontology (DO), Human Phenotype Ontology (HPO) and Medical Subject Headings (MeSH) for easy access.
(iv) Besides the SNP-trait association, we also collect SNP-Drug Response data.
(v) Comprehensive and interactive user interface to facilitate the GWAS research.

You are recommended to use Firefox, Chrome, Safari or Internet Explorer 10+ to get a better performance of GWASdb.

Link: http://jjwanglab.org/gwasdb

Operating Institution: Bioinformatic Department - University of Hong Kong 

Mutation Taster is an online tool to perform mutation predictions on a gene, cDNA, or an ORF to see what changes will occur. 

Link: http://www.mutationtaster.org/

Operating Institution: Charité - Universitätsmedizin Berlin

Tutorial:

FAQ Page

Text Tutorials

Mutation Examples

PHI-base (Pathogen Host Interactions) is a database collecting information on the genes and proteins involved in the interactions that occur between hosts and the pathogenic organisms that infect them. PHI-base collects information on genetic variations of the host and pathogens, disease states where interactions are know, taxonomic information of pathogens, orthologous and parologus genes involved in infection between species, and potential chemical compounds to interfere with the infection process.

Link: http://www.phi-base.org/

Operating Institution: Rothamsted Research 

Supporting Institution(s): Biotechnology and Biological Sciences Research Council

The Human Autophagy Database is a collection of the genes and pathways involved in the process of autophagy. The database is searchable base on gene name, protein name or abbreviation, chromosome, and function allowing for easy and rapid identification. 

Link: http://autophagy.lu/index.html

Operating Institution(s): Laboratory of Experimental Cancer Research

Supporting Institution(s): DNA Database of Japan, Luxembourg Institute of Health

Tutorials: