Databases and Genome Browsers

Abstract

The advent of the human genome project and subsequent projects to sequence genomes of other species and multiple individuals has driven the need for tools that can visualize vast amounts of genomics data. Software for genome browsing has had a vast impact in the arenas of human medical and genetics research, enabling researchers to process and integrate different data types from a large variety of sources. Three major genome browsers are freely accessible online — the University of California, Santa Cruz (UCSC) Genome Browser, the Wellcome Trust Sanger Institute (WTSI)/European Bioinformatics Institute (EBI) Ensembl browser and the National Center for Biotechnology Information (NCBI) MapViewer. The UCSC Genome Browser is a key part of the UCSC Genome Bioinformatics suite of integrated tools that facilitate data mining, together with allowing users to visualize and query their own data in the context of the existing Genome Browser annotations. The chapter provides an overview of the types of annotation data displayed by the Genome Browser, as well as step-by-step examples illustrating how to create custom tracks and query both the Genome Browser and Table Browser. The Genome Browser offers links to several programs: BLAT for performing fast sequence alignment to genomes; the In Silico PCR tool for aligning primers to the genome, and liftOver for converting genomic coordinates from one assembly to another. Other tools in the suite include the Gene Sorter for sorting genes based on their relationships such as expression profiles and genomic proximity; the Proteome Browser, which shows protein-related information in graphical form and links out to external protein-related sites; and Genome Graphs, which allows the user to display genome-wide datasets such as those from SNP association studies, linkage studies and homozygosity mapping. The suite of UCSC Genome Bioinformatics tools, data downloads, extensive documentation and links to further training materials can be found at http://genome.ucsc.edu.