A comprehensive list of databases under the following categories have been included in the annual NAR Database Summary Paper Category List :
The Online Bioinformatics Resources Collection (OBRC) contains annotations and links for thousands of bioinformatics databases and software tools. Developed by the Health Sciences Library at the University of Pittsburgh.
The National Center for Biotechnology Information provides analysis and retrieval resources that include GeneBank, Entrez, MyNCBI, PubMed, BLAST, Electronic PCR, Cancer Chromosomes, among many others.
The European Bioinformatics Institute is the European node for collecting and disseminating biological data. Some of its tools are: BLAST or FASTA programs for sequence similarity- homology analysis; InterProScan for motifs analysis; ClustalW2 for sequence alignment; MSDfold for protein structure query and comparison.
"The Cancer Genome Atlas (TCGA), a collaboration between the National Cancer Institute (NCI) and National Human Genome Research Institute (NHGRI), aims to generate comprehensive, multi-dimensional maps of the key genomic changes in major types and subtypes of cancer."
"The cBioPortal for Cancer Genomics provides visualization, analysis and download of large-scale cancer genomics data sets."
"CellMiner™ is a web application generated by the Genomics & Bioinformatics Group, LMP, CCR, NCI that facilitates systems biology through the retrieval and integration of the molecular and pharmacological data sets for the NCI-60 cell lines."
SoyBase, the USDA-ARS soybean genetic database, is a comprehensive repository for professionally curated genetics, genomics and related data resources for soybean.
SALAD is a motif-based database of protein annotations for plant comparative genomics. Contains information on proteome data sets of rice, sorghum, Arabidopsis thaliana, grape, a lycophyte, a moss, algae, and yeast.
The Plant Transcription Factor Database (PlnTFDB) provides putatively complete sets of transcription factors (TFs) and other transcriptional regulators in plant species whose genomes have been completely sequenced and annotated.
The Plant microRNA Database (PMRD) integrates available plant miRNA data deposited in public databases, collected from the literature, and data generated in-house.