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Bioinformatics: Databases

Current and relevant information resources on Bioinformatics.

Nucleic Acids Research (NAR) Database Summary

A comprehensive list of databases under the following categories have been included in the annual  NAR Database Summary Paper Category List : 

RNA sequence databases
Protein sequence databases
Structure Databases
Genomics Databases (non-vertebrate)
Metabolic and Signaling Pathways
Human and other Vertebrate Genomes
Human Genes and Diseases
Microarray Data and other Gene Expression Databases
Proteomics Resources
Other Molecular Biology Databases
Organelle databases
Plant databases
Immunological databases
Cell biology

The Online Bioinformatics Resources Collection

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.

NCBI Databases

   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.

European Bioinformatics Institute

 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 Brower

"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."

Plant-related Databases

 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.

UCSC Genome Browser

UCSC Genome Bioinformatics Site contains the reference sequence and working draft assemblies for a large collection of genomes. It also provides portals to the ENCODE and Neandertal projects.

Arabidopsis

Araport is a one-stop-shop for Arabidopsis thaliana genomics. Araport offers gene and protein reports with orthology, expression, interactions and the latest annotation, plus analysis tools, community apps, and web services. Araport is 100% free and open-source. Registered members can save their analysis, publish science apps, and post announcements.”

Bioinformatics Core

The Bioinformatics Core at Discovery Park supports research and learning in bioinformatics at Purdue through expert consultation, analysis, computational resources, classes and seminars, and grant support. Visit the BI Core website or contact director, Dr. Jyothi Thimmapuram, for more information!