Learn to use VISTA from the Genomics Division of Lawrence Berkeley National Laboratory. VISTA provides a way to examine the data from many genomes, with extensive annotation for various data types including known genes, predicted genes, SNPs, comparative multi-species analysis and much more. VISTA also contains excellent sequence alignment and visualization tools with capacity for long sequences. Use VISTA as a primary resource for your comparative genomics research needs.
You will learn:
This tutorial is a part of the tutorial group Alignment and comparison resources. You might find the other tutorials in the group interesting:
ClustalW2: Performs multiple sequence alignments
BLAST: Basic Local Alignment and Search Tool
FASTA: FASTA sequence algorithm
Entrez Gene: NCBI's Entrez tool for gene-centric information
Primer3: Pick primers from a DNA sequence.
DCODE: DCODE.org Comparative Genomics Developments, a collection of powerful comparative genomics tools
RefSeq: Provides molecular sequence records to help locate gene and protein data.
Algorithms and Analysis : This category contains various tools that may help perform analysis of different genomics data types. This may include sequence alignment, large-scale or complex queries, motif finding, or comparative assessments.
Expression : This category may contain various expression data collections, annotation tools, or repositories of expression data.
Nucleotides : Tools that are primarily used in the storage, retrieval, or exploration of nucleotide-based data. Some tools may also involve protein sequence information.
Variation & Medical : Resources that include information about sequence variation, phenotypes, or medically-relevant conditions.
Tip of the Week: Plant comparative genomics using Plaza: Plaza, a resource for plant comparative genomics, has a lot more than meets the eye at first. Currently the database has comparative tools and data for nearly 2 dozen plants including monocots, dicots...
Tip of the Week: Dot Plots, Synteny at VISTA: VISTA has added a couple of new features to their great comparative genomics resource, dot plots and synteny browser. They are excellent features and additions, but they are not yet easy to find from ...
Tip of the Week: Melina II for promoter analysis: One of the most frequently-asked questions we get when we are out doing workshops is: how do I find motifs in promoters, and what can I do with them to find more information? Just last Friday we were ...
PSA: VISTA servers down: LBL servers are down today. If you've been trying to use VISTA (the comparative genomics tools) , you will get a "server not found" error. We've contacted someone over there and were informed they wer...
Tip of the Week: VISTA Enhancer Browser: At the recent (and excellent) Beyond the Genome 2010 conference, Len Pennachio gave a talk about the VISTA Enhancer Browser that reminded me how much I have always liked this project. It's the kind of...
Recent BioMed Central research articles citing this resource
Wilken S Matthew et al., DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements. Epigenetics Chromatin (2015) doi:10.1186/1756-8935-8-8
Magi Alberto et al., Characterization and identification of hidden rare variants in the human genome. BMC Genomics (2015) doi:10.1186/s12864-015-1481-9
Roubille Camille et al., Meniscal extrusion promotes knee osteoarthritis structural progression: protective effect of strontium ranelate treatment in a phase III clinical trial. Arthritis Research Therapy (2015) doi:10.1186/s13075-015-0579-4
Zerbino R Daniel et al., The Ensembl Regulatory Build. Genome Biology (2015) doi:10.1186/s13059-015-0621-5
Haesen J et al., Use of bispectral index EEG monitoring for a fast and reliable detection of epileptic activity in postcardiac arrest patients 35th International Symposium on Intensive Care and Emergency Medicine 35th International Symposium on Intensive Care and Emergency Medicine. Critical Care (2015) doi:10.1186/cc14514