LBNL VISTA
Category Cross-Omics>Sequence Analysis/Tools
Abstract VISTA is a comprehensive suite of programs and databases for comparative analysis of genomic sequences.
There are two (2) ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre- computed whole-genome alignments of different species.
VISTA Servers --
mVISTA - mVISTA is a set of programs for comparing DNA sequences from two or more species up to mega-bases long and visualize these alignments with annotation information.
mVISTA has a clean output, allowing for easy identification of sequence similarities and differences, and is easily configurable, enabling the visualization of alignments of various lengths at different levels of resolution.
It is implemented as an on-line server that provides access to global pairwise, multiple and global (global with rearrangements) alignment tools.
Stand-alone components (AVID and visualization module mVISTA) can be downloaded from the mVISTA Web site and used on your own computer.
Alignment Programs behind mVISTA --
AVID - AVID is a program for globally aligning DNA sequences of arbitrary length.
The key features of the algorithm are that it can align hundreds of kilo- bases quickly, its accuracy and ability to detect weak homologies, and its ability to handle one of the sequences in draft (by ordering and orienting the contigs automatically).
The program works by recursively finding strong anchors from the collection of maximal matches in the sequences.
LAGAN - LAGAN is a program for global pairwise and multiple sequence alignment of finished sequences or ordered and oriented draft merged in one contig.
LAGAN performs progressive pairwise alignments, guided by a phylogenetic tree.
Alignments are aligned to other alignments using the sum-of-pairs metric.
Shuffle-LAGAN - Shuffle-LAGAN is a global alignment algorithm that is able to find rearrangements (inversions, transpositions and some duplications) in a global alignment framework.
It uses CHAOS local alignments to build a map of the rearrangements between the sequences, and LAGAN to align the regions of conserved synteny.
Note: LAGAN tools for sequence alignment were developed at Stanford by Michael Brudno and colleagues in Serafim Batzoglou's group; the development of Shuffle-LAGAN was done in collaboration with the VISTA team at LBNL.
mVISTA visualization module - The mVISTA visualization module is designed to display global sequence alignments of genomic sequences from different species.
It determines the percent identity between two sequences using a sliding window of predefined length, and displays it as a continuous curve. The program also identifies and colors regions of high conservation.
rVISTA (regulatory VISTA) - rVISTA combines searching the major 'transcription binding' site database TRANSFAC Professional from Biobase (see G6G Abstract Number 20121) with a comparative sequence analysis.
It can be used directly or through links in mVISTA, Genome VISTA, or VISTA Browser.
Genome VISTA - Genome VISTA is an automatic server that allows the user to find candidate orthologous regions for a draft or finished DNA sequence from any species on a base genome, and provides detailed comparative analysis.
You can currently align your sequence to the following base genomes: human, mouse, rat, and Drosophila Melanogaster. The manufacturer is constantly working on expanding the list of base genomes.
Genome VISTA uses a computational strategy where query sequence contigs are anchored on the base genome by local alignment matches and then globally aligned to candidate regions by the AVID program.
PHYLO-VISTA - PHYLO-VISTA is an interactive tool for analyzing multiple DNA sequence alignments by visualizing a similarity measure for DNA sequences for different species while considering their phylogenic relationships.
Features include multiple-resolution visualization for examining an alignment and easy comparison of any sub-tree of sequence data within the complete alignment dataset.
wgVISTA - wgVISTA is a set of programs for comparing DNA sequences from two ‘microbial species’ up to 10 mega-bases long and visualize these alignments with annotation information.
It is implemented as an on-line server that provides access to the 'whole-genome alignment pipeline'. The alignment program behind the pipeline is Shuffle-LAGAN (see above).
wgVISTA visualization module is the VISTA Browser (see below).
Pre-computed Whole Genome Alignments --
Vista Browser - Vista Browser is an interactive Java applet designed to visualize multiple large-scale alignments. The browser's clean display makes it easy to identify regions of high conservation across multiple species.
The browser is used to visualize pairwise and multiple whole genome alignments produced internally as well as alignments produced for GenomeVISTA users who submit their own sequences to be aligned to base genomes such as human, mouse, rat, drosophila, etc.
Whole Genome rVISTA - Whole Genome rVISTA evaluates which conserved between pairs of species transcription factor binding sites (TFBS) are over-represented in upstream regions in a group of genes.
Microbial genomes - Pre-computed full scaffold alignments for 'microbial genomes' are available as the VISTA component of IMG (Integrated Microbial Genomes) developed at the DOE Joint Genome Institute.
System Requirements
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Manufacturer
VISTA family of tools has been developed and hosted at the Genomics Division of Lawrence Berkeley National Laboratory (LBNL).
Manufacturer Web Site LBNL VISTA
Price Contact manufacturer.
G6G Abstract Number 20405
G6G Manufacturer Number 104035