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Click a theme you like to change the look of your browser. Or, if you want to find more themes, click the Get more themes link in the sidebar to go to the themes section of addons.opera.com/. From there, you can browse and install themes created by the Opera community.
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Personalize Chrome on your computer with a fun theme. The theme appears around the border of the browser and as the background when you open a new tab. Your Chrome themes are stored in your Google Account, so when you sign in to Chrome on any computer, you see the same theme.
As vertebrate 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.
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.
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.
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.
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.
Pack mode can be used to display a larger number of snake tracks in the limited vertical browser. This mode eliminates the adjacencies from the display and forces the segments onto as few rows as possible, given the constraint of still showing duplications in the query sequence.
Track display modes may be set individually or as a group on the Genome Browser Track Configurationpage. To access the configuration page, click the configure button on the annotation trackspage or the configure tracks and display button on the Gateway page. Exercise caution whenusing the show all buttons on track groups or assemblies that contain a large numbertracks; this may seriously impact the display performance of the Genome Browser or cause yourInternet browser to time out.
Filter and configuration settings are persistent from session to session on the same web browser.To return the Genome Browser display to the default set of tracks (but retain custom tracks andother configured Genome Browser settings), click the default tracks button on the GenomeBrowser tracks page. To remove all user configuration settings and custom tracks, and completelyrestore the defaults, click the "Reset All User Settings" under the top blue GenomeBrowser menu.
The first time the annotation track window is displayed, or after the Genome Browser has been reset,the size of the track window is set by default to the width that best fits your Internet browserwindow. If you horizontally resize the browser window, you can automatically adjust the annotationtrack image size to the new width by clicking the resize button under the track image. Tomanually override the default width, enter a new value in the image width text box on theTrack Configuration page, then click the submit button. The maximum supported width is 5000pixels.
To use the right-click feature, make sure your internet browser allows the display ofpopup windows from genome.ucsc.edu. When enabled, the right-click navigation feature replaces thedefault contextual popup menu typically displayed by the Internet browser when a user right-clickson the tracks image. A few combinations of the Mozilla Firefox browser on Mac OS do not support theright-click menu functionality using secondary click; in these instances, ctrl+left-click must beused to display the menu.
To print or save the image to a file: In the blue navigation bar at the top of the screen, from the "View" menu, click the "PDF/PS" link. Click one of the PDF or EPS links.NOTE: If you have configured your browser image to use one of the larger font sizes, the text in theresulting screen shot may not display correctly. If you encounter this problem, reduce the GenomeBrowser font size using the Configuration utility, then repeat thesave/print process.
For large batch jobs or internal parameter changes, it is best to install command line BLAT on yourown Linux server. Sources and executables are free for academic, personal, and non-profit purposes.BLAT source may be downloaded from -test.gi.ucsc.edu/~kent/src/(look for the blatSrc*.zip file with themost recent date). For BLAT executables, go to -test.soe.ucsc.edu/~kent/exe/; binaries are sorted by platform.Non-exclusive commercial licenses are available from the Kent Informatics website.
The Table Browser provides text-based accessto the genome assemblies and annotation data stored in the Genome Browser database. As a flexiblealternative to the graphical-based Genome Browser, this tool offers an enhanced level of querysupport that includes restrictions based on field values, free-form SQL queries, and combinedqueries on multiple tables. Output can be filtered to restrict the fields and lines returned, andmay be organized into one of several formats, including a simple tab-delimited file that can beloaded into a spreadsheet or database as well as advanced formats that may be uploaded into theGenome Browser as custom annotation tracks. The Table Browser provides a convenient alternative todownloading and manipulating the entire genome and its massive data tracks. (See theDownloading Genome Data section.)
The Sessions tool allows users to configuretheir browsers with specific track combinations, including custom tracks, and save the configurationoptions. Multiple sessions may be saved for future reference, for comparison of scenarios or forsharing with colleagues. Saved sessions will not be expired,however we still recommend that you keep local back-ups of your session contents and any associatedcustom tracks. User-generated tracks can be savedwithin sessions. 2b1af7f3a8