The UCSC Genome Browser and other visualization tools, such as Ensembl and GBrowse are widely used by researchers for viewing these genomic annotations. As the size and coverage of the human genome assembly increased, the focus turned from accumulating and assembling sequence to identifying and mapping functional landmarks, such as known genetic markers, genes, points of regulation and cytological features such as centromeres and telomeres. The UCSC Genome Browser ( ) was created to provide a graphical viewpoint on the very large amount of genomic sequence produced by the Human Genome Project. Support for high-throughput sequencing extends to compact, indexed data formats, such as BAM, bigBed and bigWig, allowing rapid visualization of large datasets from RNA-seq and ChIP-seq experiments via local hosting. Binary Alignment/Map (BAM), Variant Call Format and the Personal Genome Single Nucleotide Polymorphisms (SNPs) data formats are useful for visualizing a large sequencing experiment (whole-genome or whole-exome), where the differences between the data set and the reference assembly may be displayed graphically. The Saved Session feature allows users to store and share customized views, enhancing the utility of the system for organizing multiple trains of thought. The Table Browser is a full-featured graphical interface, which allows querying, filtering and intersection of data tables. Private data uploaded as Custom Tracks and Data Hubs in many formats may be displayed alongside the rich compendium of precomputed data in the UCSC database. The Browser also includes many other widely used tools, including BLAT, which is useful for alignments from high-throughput sequencing experiments. Gene predictions, mRNA alignments, epigenomic data from the ENCODE project, conservation scores from vertebrate whole-genome alignments and variation data may be viewed at any scale from a single base to an entire chromosome. The ability to juxtapose annotations of many types facilitates inquiry-driven data mining. Now home to assemblies for 58 organisms, the Browser presents visualization of annotations mapped to genomic coordinates. Since the early days of the Human Genome Project, it has presented an integrated view of genomic data of many kinds. The UCSC Genome Browser ( ) is a graphical viewer for genomic data now in its 13th year.
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