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
Capra A John et al., Extrapolating histone marks across developmental stages, tissues, and species: an enhancer prediction case study. BMC Genomics (2015) doi:10.1186/s12864-015-1264-3
Gularte-Mérida Rodrigo et al., Overlapping mouse subcongenic strains successfully separate two linked body fat QTL on distal MMU 2. BMC Genomics (2015) doi:10.1186/s12864-014-1191-8
Su Yu-Ching et al., Comparative genomic analysis reveals distinct genotypic features of the emerging pathogen Haemophilus influenzae type f Prokaryote microbial genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-38
Qian Cheryl Zhenyu et al., Fluency of visualizations: linking spatiotemporal visualizations to improve cybersecurity visual analytics. Security Informatics (2014) doi:10.1186/s13388-014-0006-4
Bloch Ølgaard Lars et al., Imaging of carotid artery vessel wall edema using T2-weighted cardiovascular magnetic resonance. Journal of Cardiovascular Magnetic Resonance (2014) doi:10.1186/1532-429X-16-22