The UCSC Genome Bioinformatics website provides both graphical and text-based views of the sequence data and annotations.
The Genome Browser—accessed via the Genome Browser link on the home page—is a rapid interactive interface to the data at varying levels of detail. In response to a user's query, the Genome Browser displays a set of annotations tracks corresponding to the assembly and range dictated by the query and configured based on user preferences. Alternatively, the BLAT search tool can be used to quickly search for homologous regions to a DNA or protein sequence, which can then be displayed in the browser. The user can navigate through the assembly and zoom the image in or out using navigation buttons. A set of track controls allows the user to display each annotation in single line (dense) or expanded (full) mode or hide the track completely. Some tracks have filters to fine-tune the data displayed. Individual entries within a track have associated details pages that provide information about the annotation, related links to outside sites and database, and in some cases links to the genomic, mRNA and protein sequence.
At the chromosome level (Fig. ), the Genome Browser display provides an overview of the coverage and completeness for the region. At a zoomed in level (Fig. ), the display can focus on a specific area of research interest, for example the examination of alternative splicing patterns of a gene. Most annotation tracks are displayed in a horizontal linear fashion, with the exception of a few ‘wiggle’ tracks that plot the feature's scores on a vertical axis.
Figure 1 Screenshot of the Genome Browser annotation tracks display showing a view of an entire chromosome, human chr7 from the June 28, 2002 assembly. This level of detail provides an overview of the coverage and completeness for the region. The red section (more ...)
Figure 2 A zoomed-in view of the same chromosome shown in Figure . The finer level of detail pinpoints the location of individual features in the annotation tracks. In the mRNA and RefSeq Genes gene prediction tracks, aligning regions (usually (more ...)
The Genome Browser menu bar provides access to the BLAT search tool, the DNA sequence underlying the features in the annotation tracks graphic, a coordinate conversion tool for locating the position of a feature in a different release of a genome, and user documentation. The menu bar also contains direct links to the complementary annotation in the Ensembl Genome Browser and NCBI's Entrez MapView.
The Table Browser—accessed through the Tables link on the UCSC Genome Bioinformatics home page—furnishes an alternative text-based view of the data. This tool provides access to both positional and non-positional tables, and offers an enhanced level of query support that includes free-form SQL queries and restrictions based on field values. Output can be filtered to restrict which fields and lines are returned, and may be organized into one of several formats, including a simple tab-delimited file that can be loaded into a spreadsheet or database and then processed to produce the data format suitable for a custom annotation track.
The Downloads link on the UCSC Genome Bioinformatics home page offers a convenient interface for downloading current and archived sequence and annotation data. Data can also be downloaded via ftp at ftp://genome.cse.ucsc.edu/goldenPath/
. Zipped data for each genome assembly is organized into three folders. BigZips
contains the sequence data, which is packaged by chromosome and by contig. Files ending in suffix .fa
contain the sequence in Fasta format for the contig layout. Files with suffix .agp
contain an index that shows how the corresponding .fa
file is built, with each line representing an actual sequence record or a gap. The Chromosomes
folder contains the assembled sequence in Fasta format divided up by chromosome. The Database
folder contains the genome annotation database tables in tab-delimited format.
A large portion of the Genome Browser Database is accessible using the Distributed Annotation Service (DAS) protocol (12
). The UCSC DAS server is located at http://genome.ucsc.edu/cgi-bin/das
. To accommodate the large size of some of the annotation tables, it is best to enable compression on DAS clients when accessing the UCSC DAS server.
In addition to the browsing tools, the UCSC Genome Bioinformatics home page provides links to the BLAT alignment tool, user and technical documentation, the Genome Browser mirror sites and archives, and acknowledgements to the many people who have contributed to the Genome Browser Database.