VISTA is a collection of databases, tools, and servers that permit extensive comparative genomics analyses.

Background

The VISTA family of tools is developed and hosted at Genomics Division of Lawrence Berkeley National Laboratory

Lawrence Berkeley National Laboratory

The Lawrence Berkeley National Laboratory , is a U.S. Department of Energy national laboratory conducting unclassified scientific research. It is located on the grounds of the University of California, Berkeley, in the Berkeley Hills above the central campus...

. This collaborative effort is supported by the Programs for Genomic Applications grant from the NHLBI

National Heart, Lung, and Blood Institute

The National Heart, Lung, and Blood Institute is a division of the National Institutes of Health, located in Bethesda, Maryland...

/NIH

National Institutes of Health

The National Institutes of Health are an agency of the United States Department of Health and Human Services and are the primary agency of the United States government responsible for biomedical and health-related research. Its science and engineering counterpart is the National Science Foundation...

 and the Office of Biological and Environmental Research, Office of Science, US Department of Energy

United States Department of Energy

The United States Department of Energy is a Cabinet-level department of the United States government concerned with the United States' policies regarding energy and safety in handling nuclear material...

.

It was developed from modules supplied by developers at UC Berkeley, Stanford, and UC Davis, and based partly on the AVID Global Alignment program.

Usage

There are multiple VISTA servers, each allowing different types of searches.

• mVISTA can be used to align and compare your sequences to those of multiple other species
• rVISTA (regulatory VISTA) combines transcription factor binding sites database search with a comparative sequence analysis,the discovery of possible regulatory transcription factor binding sites in regions of their genes of interest. It can be used directly or through mVISTA, Genome VISTA, or VISTA Browser. A database of tissue-specific human enhancers is available through VISTA Enhancer Browser.
• GenomeVISTA allows the comparison of sequences with whole genome assemblies. It will automatically find the ortholog, obtain the alignment and VISTA plot. It allows the viewing of an alignment together with pre-computed alignments of other species in the same interval.
• Phylo-VISTA allows the analysis of multiple DNA sequence alignments of sequences from different species while considering their phylogenic relationships.
• wgVISTA allows the alignment of sequences up to 10Mb long (finished or draft) including microbial whole-genome assemblies.

Researchers can use the VISTA Browser:

• to examine pre-computed alignments among a variety of species
• to submit sequences of their own (not limited by the species collection already in the database)

Genomes

There are more than 28 searchable genomes, including vertebrate, non-vertebrate, plants, fungi, algae, bacteria, and others. More are continually being added. These include:

• Human—Orangutan—Rhesus—Marmoset—Horse—Dog—Mouse—Rat—Chicken
• Drosophila spp.
• Arabidopsis—Rice—Sorghum
• E. coli—mycoplasma—nitrosomonas

Collaboration with other projects

Pre-computed full scaffold alignments for microbial genomes are available as the VISTA component of IMG (Integrated Microbial Genomes System

Integrated Microbial Genomes System

The Integrated Microbial Genomes is a genome browsing and annotation system developed by the DOE-Joint Genome Institute. IMG contains all the draft and complete microbial genomes sequenced by the DOE-JGI integrated with other publicly available genomes...

) developed in the DOE (Department of Energy's) Joint Genome Institute

Joint Genome Institute

The U.S. Department of Energy Joint Genome Institute was created in 1997 to unite the expertise and resources in genome mapping, DNA sequencing, technology development, and information sciences pioneered at the DOE genome centers at Lawrence Berkeley National Laboratory , Lawrence Livermore...

.

External links

• VISTA -- official VISTA site at Lawrence Berkeley National Laboratory
• VISTA tutorial and training materials -- hosted by OpenHelix, sponsored by Lawrence Berkeley National Laboratory