Bioinformatics Resources and Tools

The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery.

The European Nucleotide Archive (ENA) provides a comprehensive record of the world's nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation.

DNA Data Bank of Japan (DDBJ) Center collects nucleotide sequence data as a member of INSDC (International Nucleotide Sequence Database Collaboration) and provides freely available nucleotide sequence data and supercomputer system, to support research activities in life science.

Entrez Gene provides a unified query environment for genes defined by sequence and/or in NCBI's Map Viewer. You can query on names, symbols, accessions, publications, GO terms, chromosome numbers, E.C. numbers, and many other attributes associated with genes and the products they encode.

GeneCards is a searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes. It automatically integrates gene-centric data from ~125 web sources, including genomic, transcriptomic, proteomic, genetic, clinical and functional information.

This server provides access to the program Genscan for predicting the locations and exon-intron structures of genes in genomic sequences from a variety of organisms.

A family of gene prediction programs developed at Georgia Institute of Technology

Human Gene Expression Index (HuGE Index) aims to provide a comprehensive database to aid in understanding the expression of human genes in normal human tissues.
The mRNA expression levels of thousands of genes in a collection of normal human organs were obtained using high-density oligonucleotide array technology and deposited in this public database.
The current release of the HugeIndex provides three tools with which to access and visualize the data stored within our database. These tools can display expression information about specific genes or compare multiple tissues or experiments using boolean operators or interactive scatterplots.

ExpressDB was originally a relational database containing yeast and E. coli RNA expression data. Currently, most of the datasets are downloadable.

Gene Expression Omnibus (GEO) is a database repository of high throughput gene expression data and hybridization arrays, chips, microarrays.

CisMols (Cis-regulatory Modules) is a tool that identifies compositionally predicted cis-clusters that occur in groups of co-expressed or related genes within their ortholog-pair evolutionarily conserved cis-regulatory regions.

The miRBase database is a searchable database of published miRNA sequences and annotation. All sequence and annotation data are also available for download.

TraFaC (Transcription Factor Binding Site Comparison) is a tool that identifes regulatory regions (conserved and shared cis regulatory elements) using a comparative sequence analysis approach.

TRANSFAC® provides data on eukaryotic transcription factors, their experimentally-proven binding sites, consensus binding sequences (positional weight matrices) and regulated genes.

TRANSFAC® is a unique knowledge-base containing published data on eukaryotic transcription factors and miRNAs, their experimentally-proven binding sites, and regulated genes. The extensive compilation of binding sites provides the most comprehensive data set of transcription factor – gene interactions available.