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Bioinformatics: Databases & Tools

This guide links to bioinformatics-related resources at the University of Florida and beyond. Please contact me if you need any help in finding information useful to your research or teaching programs.

Reference tools

Genomics & Bioinformatics Dictionary Research Guide contains over 1000 bionformatics-related terms with defitnitions and links to resources.

PubMed search fields description and tags can be found here.

Genbank sample record containing detailed description of each that data element or field

RefSeq accession numbers can be distinguished from GenBank accessions by their distinct prefix format of 2 characters followed by an underscore character ('_')

GEO Datasets and GEO Profiles query fields and examples

OMIM catalog search fields are sumarized in this table

Nucleotide Databases

The International Nucleotide Sequence Databases have been developed and maintained collaboratively by DNA Databank of JapanEuropean Nucleotide Archive, and GenBank.


The National Center for Biotechnology Information provides analysis and retrieval resources that include the GeneBank, Entrez, MyNCBI, PubMed, Entrez Gene, BLAST, BLAST Link (BLink), Electronic PCR, UniGene, HomoloGene, ProtEST, Cancer Chromosomes, Entrez Genomes, 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 DNA Data Bank of Japan (DDBJ) collects sequence data mainly from Japanese researchers.  


 The National BioResource Project (NBRP) is a Japanese project  for collecting, preserving and providing bioresources for use as experimental materials for life science research. It is a group of 30 databases under an integrated database-retrieval system  (BioResource World: BRW)


  miRDB hosts predicted miRNA gene targets in human, mouse, rat, dog and chicken.


 miRBase database is a searchable database of published miRNA sequences and annotation


The Cancer Genome Atlas Data Portal (TCGA) allows you search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high-throughput sequencing analysis of the tumor genomes  

Infectious diseases databases

Bacterial and Viral Bioinformatics Resource Center, an information system designed to support the biomedical research community’s work on bacterial and viral infectious diseases via integration of vital pathogen information with rich data and analysis tools

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.

Other databases

BioNumbers is a reference database of numbers in molecular and cell biology. Whenever you need the size of a cell, metabolite concentrations, reaction rates and times, number of mitocondria in a cell, etc, check this database.  


BRENDA is maintained and developed at the Institute of Biochemistry and Bioinformatics at the Technical University of Braunschweig. It is a collection of enzyme functional data available free of charge over the internet.

Subject Guide

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