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Genomics: Genome Browsers

Genome Browsers

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. It will include the genomes of about 2500 unidentified people from about 25 populations around the world.

 The Jena Prokaryotic Genome Viewer (JPGV) is a freely accessible web tool aimed at visualization and analysis of prokaryotic genomes.

 Gramene is a curated, open-source, data resource for comparative genome analysis in the grasses. Its genome browser is based on Ensemble technology.

Sol Genomics Network houses information the tomato, potato, pepper, and egg plant genome.

Main Genome Browsers

 Ensemble genome browser is a joint project between EBI- EMBL and the Wellcome Trust Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. Its goal is "to automatically annotate the genome, integrate this annotation with other available biological data and make all this publicly available via the web."

 UCSC Genomie Browser was developed by Prof. David Haussler at the University of California, Santa Cruz in 2000. It displays 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

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.

 NCBI's Map Viewer "provides special browsing capabilities for a subset of organisms. You can view and search an organism's complete genome, display chromosome maps, and zoom into progressively greater levels of detail, down to the sequence data for a region of interest".

Multiple Genomes Alignment

  Multiple Genome Alignment Mauve is a software developed by the University of Wisconsin-Madison for multiple genome alignments for those doing research on comparative genomics and the study of evolutionary dynamics. "Mauve is distributed free-of-charge for Windows, Mac OS X, and Linux. 

Genetic Prediction Programs

GeneMark is "a family of gene prediction programs developed at Georgia Institute of Technology, Atlanta, Georgia, USA.

The GeneMark.hmm for Prokaryotes and Eukaryotic GeneMark.hmm programs determine the protein-coding potential of a DNA sequence (within a sliding window) by using species specific parameters

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