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[Arleen Smelko]

Asvertebrate genome sequences near completion and research re-focuses on their analysis, the issueof effective sequence display becomes critical: it is not helpful to have 3 billion letters ofgenomic DNA shown as plain text! As an alternative, the UCSC Genome Browser provides a rapid andreliable display of any requested portion of genomes at any scale, together with dozens of alignedannotation tracks (known genes, predicted genes, ESTs, mRNAs, CpG islands, assembly gaps andcoverage, chromosomal bands, mouse homologies, and more). Half of the annotation tracks are computedat UCSC from publicly available sequence data. The remaining tracks are provided by collaboratorsworldwide. Users can also add their own custom tracks to the browser for educational or researchpurposes.

The Genome Browser stacks annotation tracks beneath genome coordinate positions, allowing rapidvisual correlation of different types of information. The user can look at a whole chromosome toget a feel for gene density, open a specific cytogenetic band to see a positionally mapped diseasegene candidate, or zoom in to a particular gene to view its spliced ESTs and possible alternativesplicing. The Genome Browser itself does not draw conclusions; rather, it collates all relevantinformation in one location, leaving the exploration and interpretation to the user.

The Genome Browser supports text and sequence based searches that provide quick, precise access toany region of specific interest. Secondary links from individual entries within annotation trackslead to sequence details and supplementary off-site databases. To control information overload,tracks need not be displayed in full. Tracks can be hidden, collapsed into a condensed orsingle-line display, or filtered according to the user's criteria. Zooming and scrolling controlshelp to narrow or broaden the displayed chromosomal range to focus on the exact region of interest.Clicking on an individual item within a track opens a details page containing a summary ofproperties and links to off-site repositories such as PubMed, GenBank, Entrez, and OMIM. The pageprovides item-specific information on position, cytoband, strand, data source, and encoded protein,mRNA, genomic sequence and alignment, as appropriate to the nature of the track.

A blue navigation bar at the top of the browser provides links to several other tools and datasources. For instance, under the "View" menu, the "DNA" link enables the userto view the raw genomic DNA sequence for the coordinate range displayed in the browser window. ThisDNA can encode track features via elaborate text formatting options. Other links tie the GenomeBrowser to the BLAT alignment tool, provide access to the underlying relational database via theTable Browser, convert coordinates across different assembly dates, and open the window at thecomplementary Ensembl orNCBI Genome Data Viewer annotation.

The browser data represents an immense collaborative effort involvingthousands of people from the international biomedical research community. The UCSC BioinformaticsGroup itself does no sequencing. Although it creates the majority of the annotation tracks in-house,the annotations are based on publicly available data contributed by many labs and research groupsthroughout the world. Several of the Genome Browser annotations are generated in collaboration withoutside individuals or are contributed wholly by external research groups. UCSC's other major rolesinclude building genome assemblies, creating the Genome Browser work environment, and serving itonline. The majority of the sequence data, annotation tracks, and even software are in the publicdomain and are available for anyone to download.

In addition to the Genome Browser, the UCSC Genome Bioinformatics group provides several other toolsfor viewing and interpreting genome data: BLAT - a fast sequence-alignment tool similar to BLAST. Read more. Table Browser - convenient text-based access to the database underlying the Genome Browser. Read more. Genome Graphs - a tool that allows you to upload and display genome-wide data sets such as the results of genome-wide SNP association studies, linkage studies and homozygosity mapping. Read more. Gene Sorter - expression, homology, and other information on groups of genes that can be related in many ways. Read more.Getting started: Genome Browser gatewayThe UCSC Genome Bioinformatics home page providesaccess to Genome Browsers on several different genome assemblies. To get started, click the Browserlink on the blue sidebar. This will take you to a Gateway page where you can select which genome todisplay. Note that there are also official mirror sites in Europe andAsia for users who are geographically closer to those continents than to the western UnitedStates.

Occasionally the Gateway page returns a list of several matches in response to a search, rather thanimmediately displaying the Genome Browser window. When this occurs, click on the item in whichyou're interested and the Genome Browser will open to that location.

The search mechanism is not a site-wide search engine. Instead, it primarily searches GenBank mRNArecords whose text annotations can include gene names, gene symbols, journal title words, authornames, and RefSeq mRNAs. Searches on other selected identifiers, such as NP and NM accessionnumbers, OMIM identifiers, and Entrez Gene IDs are supported. However, some types of queries willreturn an error, e.g. post-assembly GenBank entries, withdrawn gene names, and abandoned synonyms.If your initial query is unsuccessful, try entering a different related term that may produce thesame location. For example, if a query on a gene symbol produces no results, try entering an mRNAaccession, gene ID number, or descriptive words associated with the gene.

If you have genomic, mRNA, or protein sequence, but don't know the name or the location to which itmaps in the genome, the BLAT tool will rapidly locate theposition by homology alignment, provided that the region has been sequenced. This search will findclose members of the gene family, as well as assembly duplication artifacts. An entire set of querysequences can be looked up simultaneously when provided in fasta format.

A successful BLAT search returns a list of one or more genome locations that match the inputsequence. To view one of the alignments in the Genome Browser, click the browser link forthe match. The details link can be used to preview the alignment to determine if it is ofsufficient match quality to merit viewing in the Genome Browser. If too many BLAT hits occur, trynarrowing the search by filtering the sequence in slow mode withRepeatMasker, then rerunning the BLATsearch.

You can open the Genome Browser window with a custom annotation track displayed by using the AddCustom Tracks feature available from the gateway and annotation tracks pages. For more informationon creating and using custom annotation tracks, refer to the Creatingcustom annotation tracks section.

NOTE: If an annotation track does not display correctly when you attempt to uploadit, you may need to reset the Genome Browser to its default settings, then reload the track. Forinformation on troubleshooting display problems with custom annotation tracks, refer to thetroubleshooting section in the Creating custom annotation trackssection.

The Table Browser, a portal to the underlyingopen source MariaDB relational database driving theGenome Browser, displays genomic data as columns of text rather than as graphical tracks. For moreinformation on using the Table Browser, see the section Getting started: onthe Table Browser.

Several external gateways provide direct links into the Genome Browser. Examples include:Entrez Gene,AceView,Ensembl,SuperFamily, andGeneCards. Journal articles can also linkto the browser and provide custom tracks. Be sure to use the assembly date appropriate to theprovided coordinates when using data from a journal source.

It is usually best to work with the most recent assembly even though a full set of tracks might notyet be ready. Be aware that the coordinates of a given feature on an unfinished chromosome maychange from one assembly to the next as gaps are filled, artifactual duplications are reduced, andstrand orientations are corrected. The Genome Browser offers multiple tools that can correctlyconvert coordinates between different assembly releases. For more information on conversion tools,see the section Converting data between assemblies.

Bear in mind that the Genome Browser cannot outperform the underlying quality of the draft genome.Assembly errors and sequence gaps may still occur well into the sequencing process due to regionsthat are intrinsically difficult to sequence. Artifactual duplications arise as unavoidablecompromises during a build, causing misleading matches in genome coordinates found by alignment.

The Genome Browser annotation tracks page displays a genome location specified through a Gatewaysearch, a BLAT search, or an uploaded custom annotation track. There are five main features on thispage: a set of navigation controls, a chromosome ideogram, the annotations tracksimage, display configuration buttons, and a set of trackdisplay controls.

The first time you open the Genome Browser, it will use the application default values to configurethe annotation tracks display. By manipulating the navigation, configuration and display controls,you can customize the annotation tracks display to suit your needs. For a complete description ofthe annotation tracks available in all assembly versions supported by the Genome Browser, see the Annotation Track Descriptions section.

The Genome Browser retains user preferences from session to session within the same web browser,although it never monitors or records user activities or submitted data. To restore the defaultsettings, click the "Reset All User Settings" under the top blue Genome Browser menu. Toreturn the display to the default set of tracks (but retain custom tracks and other configuredGenome Browser settings), click the default tracks button on the Genome Browser page.

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