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
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
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
Huang Jun et al., Comparative transcriptomics uncovers alternative splicing changes and signatures of selection from maize improvement Plant genomics. BMC Genomics (2015) doi:10.1186/s12864-015-1582-5
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
Song Jimin et al., Spectacle: fast chromatin state annotation using spectral learning. Genome Biology (2015) doi:10.1186/s13059-015-0598-0