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Biological Database Analysis

BioCodeKb - Bioinformatics Knowledgebase

Biological databases are libraries of life sciences information, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. They contain information from research areas including genomics, proteomics, metabolomics, microarray gene expression, and phylogenetics. Information contained in biological databases includes gene function, structure, localization (both cellular and chromosomal), clinical effects of mutations as well as similarities of biological sequences and structures.

Ensembl provides a genome browser that acts as a single point of access to annotated genomes for mainly vertebrate species. Ensembl integrates together gene annotation, genetic variation, gene regulation data, and comparative genomics onto a single genomic platform. Gene annotation is carried out in house, annotating the full intron–exon structure of coding and noncoding transcripts. Short variants, such as SNPs and indels, are pulled into Ensembl from external databases, alongside structural variants and copy-number variants. ChIP-seq and DNase-seq data is used for in-house prediction of regions of open chromatin and regulatory elements such as promoters, enhancers and CTCF binding sites on the genome and their activity in different cell types. It is also an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements from sequence analysis to data storage and visualisation.

The UCSC site hosts a set of genome analysis tools, including a full-featured GUI interface for mining the information in the browser database, a FAST sequence alignment tool BLAT that is also useful for simply finding sequences in the massive sequence of any of the featured . The UCSC Genome Browser provides a rapid and reliable display of any requested portion of genomes at any scale, together with dozens of aligned annotation tracks (known genes, predicted genes, ESTs, mRNAs, CpG islands, assembly gaps and coverage, chromosomal bands, mouse homologies, and more).

MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. Selected sets of RNA-Seq data have been added to GXD. Heat map visualization and analysis tools for RNA-seq data now available at GXD.

The Universal Protein Resource (UniProt) provides a stable, comprehensive, freely accessible, central resource on protein sequences and functional annotation. The core activities include manual curation of protein sequences assisted by computational analysis, sequence archiving, development of a user-friendly UniProt website, and the provision of additional value-added information through cross-references to other databases.

The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cryo-electron microscopy, and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations (PDBe, PDBj, RCSB and BMRB).

The PDB is a key in areas of structural biology, such as structural genomics. The structure files may be viewed using one of several free and open source computer programs, including Jmol, Pymol, VMD, and Rasmol.

The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR).

miRBaseMiner is a Python pipeline, with accompanying R scripts for data visualization. Using miRBaseMiner, a user can specify a range of miRBase versions to be investigated and the pipeline will download the associated annotation files from the miRBase website.

Phytozome, the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute, provides JGI users and the broader plant science community a hub for accessing, visualizing and analyzing JGI-sequenced plant genomes, as well as selected genomes and datasets that have been sequenced elsewhere. All gene sets in Phytozome have been annotated with KOG, KEGG, ENZYME, Pathway and the InterPro family of protein analysis tools.

The Rat Genome Database (RGD) is the premiere location for rat genomics, genetics, physiology and functional data, as well as data for comparative genomics between rat, human and mouse. RGD is responsible for attaching biological information to the rat genome via structured vocabulary, or ontology, annotations assigned to genes and quantitative trait loci (QTL), and for consolidating rat strain data and making it available to the research community.

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We are providing “Biological Database Analysis” service to the bioinformatics community through our expertise to gain information from research areas including genomics, proteomics, metabolomics, microarray gene expression and phylogenetics through the Biological Databases.


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