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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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
Song Jimin et al., Spectacle: fast chromatin state annotation using spectral learning. Genome Biology (2015) doi:10.1186/s13059-015-0598-0
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
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
Petersen Romina et al., Columnar apple primary roots share some features of the columnar-specific gene expression profile of aerial plant parts as evidenced by RNA-Seq analysis Genetics and crop biotechnology. BMC Plant Biology (2015) doi:10.1186/s12870-014-0356-6