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.
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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
Ebbert T. W. Mark et al., Variants in CCL16 are associated with blood plasma and cerebrospinal fluid CCL16 protein levels. BMC Genomics (2016) doi:10.1186/s12864-016-2788-x
Ho Wei-Min et al., Prediction of in-hospital stroke mortality in critical care unit Medicine. SpringerPlus (2016) doi:10.1186/s40064-016-2687-2
Ishitsuka Koji et al., Diagnosis and follow-up of posterior inferior cerebellar artery dissection complicated with ischemic stroke assisted by T1-VISTA: a report of two cases Cerebrovascular disease and stroke. BMC Neurology (2016) doi:10.1186/s12883-016-0637-9
Chun Hee Eun et al., Dexmedetomidine-ketamine versus Dexmedetomidine-midazolam-fentanyl for monitored anesthesia care during chemoport insertion: a Prospective Randomized Study Perioperative medicine and outcome. BMC Anesthesiology (2016) doi:10.1186/s12871-016-0211-4
Staley A. Lyndsay et al., Genome-wide association study of prolactin levels in blood plasma and cerebrospinal fluid. BMC Genomics (2016) doi:10.1186/s12864-016-2785-0