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Biomedical Science

Bioinformatics Databases and Tools

Genome Browsers

Main Genome Browsers

Genome browsers integrate genomic sequence and annotation data from different sources and provide a platform to search, browse, retrieve, and analyze genomic data. These are the main genome browsers:

 UCSC Genome Browser provides an interactive interface for navigating several sources of genomic information including sequence variation, transcription binding sites and epigenetic modifications. In addition, UCSC has annotated genomes of some other species, including the Ebola virus, and several species of fruit flies.

NCBI Genome Data Viewer is NCBI's genome browser (previously known as NCBI Map Viewer) supporting the exploration and analysis of eukaryotic RefSeq genome assemblies. It allows users to visualize different types of sequence-associated data in a genomic context. Genome Data Viewer is also used by different NCBI resources, such as GEO, to display datasets associated with specified experiments or samples in a genome browser context.

 Ensembl hosts genomic databases and resources for comparative genomics, gene regulation, and epigenetics. It has over eighty genomes.

UCSC Genome Browser

Other Genome Browsers

 

 NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix this data with your own private data.

The Department of Energy Joint Genome Institute Genome Browser includes the Integrated Microbial Genomes and Metagenomes (IMG/M), the Fungal Genomics Resource- annotated fungal genomes, and the Phytozome -a comparative hub for green plant genomes and gene family data and analysis.

The 1000 Genomes Project is public catalog of human genetic variation, including SNPs and structural variants, and their haplotype contexts. The NCBI provides an interactive graphical viewer that allows users to explore genotype and variant calls that have been produced by the 1000 Genomes project.  

The Jena Prokaryotic Genome Viewer (JPGV) is a freely accessible web tool aimed at visualization and analysis of prokaryotic genomes. JPGV currently includes 1140 genomic elements of 293 species.

 

 

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