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human genome assemblies in August 2001, NCBI built eight reference human genome assemblies for the bioinformatics community, culminating with a final assembly in March 2006. Subsequently, an international collaboration that includes the Wellcome Trust Sanger Institute (WTSI), the Genome Institute at Washington University, EBI, and NCBI formed the Genome Reference Consortium (GRC), which took over responsibility for subsequent assemblies of the human genome. This consortium has produced two human genome assemblies, namely GRCh37 in February 2009 and GRCh38 in December 2013. As one might expect, each new genome assembly leads to changes in the sequence coordinates of annotated features. In between the release of major assemblies, GRC creates patches, which either correct errors in the assembly or add alternate loci. These alternate loci are multiple representations of regions that are too variable to be represented by a single reference sequence, such as the killer cell immunoglobulin-like receptor (KIR) gene cluster on chromosome 19 and the major histocompatibility complex (MHC) locus on chromosome 6. Unlike new genome assemblies, patches do not affect the chromosomal coordinates of annotated features. GRCh38.p10 has 282 alternate loci or patches.
While the GRC also assembles the mouse, zebrafish, and chicken genomes, other genomes are sequenced and assembled by specialized sequencing consortia. The panda genome sequence, published in 2009, was the first mammalian genome to abandon the clone-based sequencing strategies used for human and mouse, relying entirely on next generation sequencing methodologies (Li et al. 2010). Subsequent advances in sequencing technologies have led to rapid increases in the number of complete genome sequences. At the time of this writing, both the UCSC Genome Browser and the main Ensembl web site host genome assemblies of over 100 organisms. The look and feel of each genome browser is the same regardless of the species displayed; however, the types of annotation differ depending on what data are available for each organism.
The backbone of each browser is an assembled genomic sequence. Although the underlying genomic sequence is, with a few exceptions, the same in both genome browsers, each team calculates its annotations independently. Depending on the type of analysis, a user may find that one genome browser has more relevant information than the other. The location of genes, both known and predicted, is a central focus of both genome browsers. For human, at present, both browsers feature the GENCODE gene predictions, an effort that is aimed at providing robust evidence-based reference gene sets (Harrow et al. 2012). Other types of genomic data are also mapped to the genome assembly, including NCBI reference sequences, single-nucleotide polymorphisms (SNPs) and other variants, gene regulatory regions, and gene expression data, as well as homologous sequences from other organisms. Both genome browsers can be accessed through a web interface that allows users to navigate through a graphical view of the genome. However, for those wishing to carry out their own calculations, sequences and annotations can also be retrieved in text format. Each browser also provides a sequence search tool – BLAT (Kent 2002) or BLAST (Camacho et al. 2009) – for interrogating the data via a nucleotide or protein sequence query. (Additional information on both BLAT and BLAST is provided in Chapter 3.)
In order to provide stability and ensure that old analyses can be reproduced, both genome browsers make available not only the current version of the genome assemblies but older ones as well. In addition, annotation tracks, such as the GENCODE gene track and the SNP track, may be based on different versions of the underlying data. Thus, users are encouraged to verify the version of all data (both genome assembly and annotations) when comparing a region of interest between the UCSC and Ensembl Genome Browsers.
This chapter presents general guidelines for accessing the genome sequence and annotations using the UCSC and Ensembl Genome Browsers. Although similar analyses could be carried out with either browser, we have chosen to use different examples at the two sites to illustrate different types of questions that a researcher might want to ask. We finish with a short description of JBrowse (Buels et al. 2016), another web-based genome browser that users can set up on their own servers to share custom genome assemblies and annotations. All of the resources discussed in this chapter are freely available.
The UCSC Genome Browser
After starting in 2000 with just a display of an early draft of the human genome assembly, the UCSC Genome Browser now provides access to assemblies and annotations from over 100 organisms (Haeussler et al. 2019). The majority of assemblies are of mammalian genomes, but other vertebrates, insects, nematodes, deuterostomes, and the Ebola virus are also included. The assemblies from some organisms, including human and mouse, are available in multiple versions. New organisms and assembly versions are added regularly.
The UCSC Browser presents genomic annotation in the form of tracks. Each track provides a different type of feature, from genes to SNPs to predicted gene regulatory regions to expression data. Each organism has its own set of tracks, some created by the UCSC Genome Bioinformatics team and others provided by members of the bioinformatics community. Over 200 tracks are available for the GRCh37 version of the human genome assembly. The newer human genome assembly, GRCh38, has fewer tracks, as not all the data have been remapped from the older assembly. Other genomes are not as well annotated as human; for example, fewer than 20 tracks are available for the sea hare. Some tracks, such as those created from NCBI transcript data, are updated weekly, while others, such as the SNP tracks created from NCBI variant data (Sayers et al. 2019), are updated less frequently, depending on the release schedule of the underlying data. For ease of use, tracks are organized into subsections. For example, depending on the organism, the Genes and Gene Predictions section may include evidence-based gene predictions, ab initio gene predictions, and/or alignment of protein sequences from other species.
The home page of the UCSC Genome Browser provides a stepping-off point for many of the resources developed by the Genome Bioinformatics group at UCSC, including the Genome Browser, BLAT, and the Table Browser, which will be described in detail later in this chapter. The Tools menu provides a link to liftOver, a widely used tool that converts genomic coordinates from one assembly to another. Using this tool, it is possible to update annotation files so that old data can be integrated into a new genome assembly. The Download menu provides an option to download all the sequence and annotation data for each genome assembly hosted by UCSC, as well as some of the source code. The What's New section provides updates on new genome assemblies, as well as new tools and features. Finally, there is an extensive Help menu, with detailed documentation as well as videos. Users may also submit questions to a mailing list, and most queries are answered within a day.
The UCSC Genome Browser provides multiple ways for both individual users and larger genome centers to share data with collaborators or even the entire bioinformatics community. These sharing options are available on the My Data link on the home page. Custom Tracks allow users to display their own data as a separate annotation track in the browser. User data must be formatted in a standard data structure in order to be interpreted correctly by the browser. Many commonly used file formats are supported, including Browser Extensible Data (BED), Binary Alignment/Map (BAM), and Variant Call Format (VCF; Box 4.1). Small data files can be uploaded or pasted into the Genome Browser for personal use. Larger files must be saved on the user's web server and accessed by URL through the Genome Browser. As anyone with the URL can access the data, this method can be used to share data with collaborators. Alternatively, Custom Tracks, along with track configurations and settings, can be shared with selected collaborators using a named Session. Some groups choose to make their Sessions available to the world at large in My Data → Public Sessions. Finally, groups with very large datasets can host their data in the form of a Track Hub so that it can be viewed on the UCSC Genome Browser. When a Track Hub is paired with an Assembly Hub, it can be used to create a browser for a genome assembly not already hosted by UCSC.
Box 4.1 Common File Types for Genomic Data
Both the UCSC and Ensembl Genome Browsers allow users to upload their own data so that they