The main tables are named chain OtherDb, and auxiliary "chainLink" tables are named chain OtherDbLink. Therefore, splitting does not apply to such assemblies, and a track named foo would have one table named foo.Ĭhain tracks use two different types of database table to efficiently store the usually quite large amounts of data. WGS scaffolds), then it would kill MySQL to make one table per sequence for each split track. On the other hand, if an assembly consists of thousands of separate unplaced sequences (e.g. For example, if a track named foo is split, its database tables are named chr*_foo (or using the MySQL wildcard, chr%\_foo). When split, table names for a track end with the same track name, prefixed by the sequence name and _. This applies to the Chain tracks but not Net tracks, since Chain tracks contain much more data.
a few dozen chromosomes or mapping groups, possibly with concatenated unplaced sequences in virtual "chromosomes"), a track's data may be split into per-sequence tables instead of kept in one main table. Naming of database tables for comparative genomics tracksįor assemblies that consist of a reasonably small number of sequences (e.g. UCSC's annotations for human refer to chr1, chr2, chr3 etc., and for worm, chrI, chrII, chrIII etc.
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UCSC prefixes those sequence names with "chr", to make it easier for its software to recognize chromosome sequence names. Most genome assemblies use sequence names for chromosomes that match chromosome designations in the literature - for example, 1, 2, 3 for human, and I, II, III for worm. Then, in order to avoid name clashes among the deluge of newly sequenced species, a new convention was established: when new species are added to the browser, we use the first three letters of the genus in lowercase, and first three letters of the species with the first letter capitalized (e.g. melanogaster (dm) and several other species added before mid-2003. That convention was followed for rat (rn), C. The next species added to the browser was mouse, and the first letters of its genus and species names were used: "mm" for Mus musculus. For example, hg18 is the database of annotations for the 18th assembly of the human genome displayed in the UCSC Genome Browser the assembly itself is better known as NCBI Build 36. Jim Kent wrote the UCSC Genome Browser while working on the Human Genome Project, so all databases for the human genome start with "hg". The database name begins with 2 or 6 letters indicating the species, followed by a sequence number which usually starts with 1 on the first assembly that UCSC processes.
Each database contains at least one table for each "track" (set of annotations).
UCSC builds a separate MySQL database of annotations for each genome assembly. UCSC naming conventions and other relevant subtletiesĪn understanding of UCSC conventions is not really a prerequisite, but will be quite helpful for understanding the installation process. Here are some example approximate sizes for various tracks and organisms (note that each genome assembly usually has many Chain and Net tracks, and one Conservation track):
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4.6 Download and install the GBrowse plugin(s).4.5 Conservation track only: download external files.4.3 Download mysql dump files from UCSC.4.2 Which tables for my track(s) of interest?.2.3 Naming of database tables for comparative genomics tracks.2 UCSC naming conventions and other relevant subtleties.
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