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Read more about your university SSO profile. To access filter and configuration options for a specific annotation track, open the tracks’ description page by clicking the label for the track’s control menu under the Track Controls section, the mini-button to the left of the displayed track, or the «Configure The filter and configration section is located at the top of the description page.
In most instances, more information about the configuration options is available within the description text or through a special help link located in the configuration section.
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 and other configured Genome Browser settings , click the default tracks button on the Genome Browser tracks page. To remove all user configuration settings and custom tracks, and completely restore the defaults, click the «Click here to reset» link on the Genome Browser Gateway page.
Zooming and scrolling the tracks display At times you may want to adjust the amount of flanking region displayed in the annotation tracks window or adjust the scale of the display. At a scale of 1 pixel per base pair, the window accurately displays the width of exons and introns, and indicates the direction of transcription using arrowheads for multi-exon features. At a grosser scale, certain features – such as thin exons – may disappear. Also, some exons may falsely appear to fall within RepeatMasker features at some scales.
Click the zoom in and zoom out buttons at the top of the Genome Browser page to zoom in or out on the center of the annotation tracks window by 1. Alternatively, you can zoom in 3-fold on the display by clicking anywhere on the Base Position track. In this case, the zoom is centered on the coordinate of the mouse click. To view the base composition of the sequence underlying the current annotation track display, click the base button.
Quickly zoom to a specific region of interest by using the browser’s «drag-and-select» feature. To define the region you wish to zoom to, click and hold the mouse button on one edge of the desired zoom area in the Base Position track, drag the mouse right or left to highlight the selection area, then release the mouse button.
A «drag-and-select» popup will appear. Click on the «Zoom In» button to zoom in on the selected region. To disable the drag-and-select popup, check the «Don’t show this dialog again and always zoom» checkbox.
To drag-and-select zoom on a part of the image other than the Base Position track, depress the shift key before clicking and dragging the mouse.
The view may be scrolled by up to one image width. It is also possible to scroll the left or right side of the tracks by a specified number of vertical gridlines while keeping the position of the opposite side fixed.
To do this, click the appropriate move start or move end arrow, located under the annotation tracks window. For example, to keep the left-hand display coordinate fixed but increase the right-hand coordinate, you would click the right-hand move end arrow. To increase or decrease the gridline scroll interval, edit the value in the move start or move end text box. Highlighting a region The browser’s «drag-and-select» feature also allows you to highlight a region or gene of interest.
To highlight a region, click and hold the mouse button on one edge of the desired area to be highlighted in the Base Position track, drag the mouse right or left to highlight the selection area, then release the mouse button. Click the «Highlight» button on the «drag-and-select» popup. Note, if the «drag-and-select» popup has been disabled, you may re-enable it on the browser image ‘configure’ page by selecting «Enable highlight with drag-and-select if unchecked, drag-and-select always zooms to selection «.
Options to remove highlighting, zoom in to a highlighted region, or jump to a highlighted region, can be found on the browser’s right-click menu. To highlight a gene of interest, right-click on the gene e. For more information on valid entries for this text box, refer to the Getting Started section. If a chromosome image ideogram is available above the track display, click anywhere on the chromosome to move to that position the current window size will be maintained.
Select a region of any size by clicking and dragging in the image. Finally, hold the «control» key while clicking on a chromosome band to select the entire band. Changing the order of the displayed tracks To vertically reposition a track in the annotation track window, click-and-hold the mouse button on the side label, then drag the highlighted track up or down within the image.
Release the mouse button when the track is in the desired position. To move an entire group of associated tracks such as all the displayed subtracks in a composite track , click-and-hold the gray mini-button to the left of the tracks, then drag. Changing the width of the annotation track window 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 browser window.
If you horizontally resize the browser window, you can automatically adjust the annotation track image size to the new width by clicking the resize button under the track image. To manually override the default width, enter a new value in the image width text box on the Track Configuration page, then click the submit button. The maximum supported width is pixels. Changing the width of the label area to the left of the image The item labels or track label, when viewed in dense mode are displayed to the left of the annotation image.
The width of this area is set to 17 characters by default. To change the width, edit the value in the label area width text box on the Track Configuration page, then click Submit. Changing the text size in the annotation track image The annotation track image may be adjusted to display text in a range of fonts from «tiny» to «huge». To change the size of the text, select an option from the text size pull-down menu on the Track Configuration page, then click Submit.
The text size is set to «small» by default. Hiding the annotation track labels The track and element labels displayed above and to the left of the tracks in the annotation tracks image may be hidden from view by unchecking the Display track descriptions above each track and Display labels to the left of items in tracks boxes, respectively, on the Track Configuration page.
Hiding the display grid on the annotation tracks image The light blue vertical guidelines on the annotation tracks image may be removed by unchecking the Show light blue vertical guidelines box on the Track Configuration page. Hiding the chromosome ideogram The chromosome ideogram, located just above the annotation tracks image, provides a graphical overview of the features on the selected chromosome, including its bands, the position of the centromere, and an indication of the region currently displayed in the annotation tracks image.
To hide the ideogram, uncheck the Display chromosome ideogram above main graphic box on the Tracks Configuration page. Clicking on the gray arrows shifts the image window toward that end of the chromosome so that the next item in the track is displayed. Clicking on one of the white arrows shifts the image window to the next exon located towards that end of the feature.
Enabling the right-click navigation feature Several of the common display and navigation operations offered on the Genome Browser tracks page may be quickly accessed by right-clicking on a feature on the tracks image and selecting an option from the displayed popup menu.
Depending on context, the right-click feature allows the user to: change the track display mode zoom in or out to the exact position coordinates of the feature open the «Get DNA» window at the feature’s coordinates display details about the feature open a popup window to configure the track’s display display the entire tracks image in a separate window for inclusion in spreadsheets or other documents.
Printing a copy of the annotation track window The Genome Browser provides a mechanism for saving a copy of the currently displayed annotation tracks image to a file that can be printed or edited. Images saved in PostScript format can be printed at high resolution and edited by drawing programs such as Adobe Illustrator. This is useful for generating figures intended for publication. To print or save the image to a file: 1.
NOTE: If you have configured your browser image to use one of the larger font sizes, the text in the resulting screen shot may not display correctly.
It may miss genomic alignments that are more divergent or shorter than these minimums, although it will find perfect sequence matches of 32 bases and sometimes as few as 22 bases. The tool is capable of aligning sequences that contain large introns. In general, gene family members that arose within the last million years can generally be detected. Some common uses of BLAT include: — finding the genomic coordinates of mRNA or protein within a given assembly — determining the exon structure of a gene — displaying a coding region within a full-length gene — isolating an EST of special interest as its own track — searching for gene family members — finding human homologs of a query from another species.
Select the genome, assembly, query type, output sort order, and output type. To order the search results based on the closeness of the sequence match, choose one of the score options in the Sort output menu.
The score is determined by the number of matches vs. If the sequence to be uploaded is in an unformatted plain text file, enter the file name in the Upload sequence text box, then click the submit file button.
Otherwise, paste the sequence or fasta-formatted list into the large edit box, and then click the submit button. Input sequence can be obtained from the Genome Browser as well as from a custom annotation track. Multiple sequences may be submitted at the same time if they are of the same type and are preceded by unique header lines. Protein or translated input sequences must not exceed 10, letters. As many as 25 multiple sequences may be submitted at the same time.
The maximum combined length of DNA input for multiple sequence submissions is 50, bases with a 25, base limit per individual sequence. For protein or translated input, the maximum combined input length is 25, letters with a letter limit per individual sequence. A BLAT query often generates multiple hits. This can happen when the genome contains multiple copies of a sequence, paralogs, pseudogenes, statistical coincidences, artifactual assembly duplications, or when the query itself contains repeats or common retrotransposons.
When too many hits occur, try resubmitting the query sequence after filtering in slow mode with RepeatMasker. Items in the search results list are ordered by the criteria specified in the Sort output menu. Each line item provides links to view the details of the sequence alignment or to open the corresponding view in the Genome Browser. The details link gives the letter-by-letter alignment of the sequence to the genome. It is recommended that you first examine the details of the alignment for match quality before viewing the sequence in the Genome Browser.
When several nearby BLAT matches occur on a single chromosome, a simple trick can be used to quickly adjust the Genome Browser track window to display all of them: open the Genome Browser with the match that has the lowest chromosome start coordinate, paste in the highest chromosome end coordinate from the list of matches, then click the jump button.
The resulting PSL track can be uploaded into the Genome Browser by pasting the data into the data text box on the Genome Browser Add Custom Tracks page, accessed via the «add custom tracks» button on the Browser gateway and annotation tracks pages. See the Creating custom annotation tracks section for more information. Sources and executables are free for academic, personal, and non-profit purposes.
Non-exclusive commercial licenses are available from the Kent Informatics website. Annotation track descriptions Detailed information about an individual annotation track, including display characteristics, configuration information, and associated database tables, may be obtained from the track description page accessed by clicking the mini-button to the left of the displayed track in the Genome Browser, or by selecting the «Open details Click the «View table schema» link on the track description page to display additional information about the primary database table underlying the track.
Table schema information may also be accessed via the «describe table schema» button in the Table Browser. For more information on configuring and using the tracks displayed in the Genome Browser track window, see the section Interpreting and Fine-tuning the Genome Browser display. Tips for viewing annotation track data — To display a description page with more information about the track, click on the mini-button to the left of a track. To restrict the browser’s display to only those tracks in which you’re interested, set the display mode of the unwanted tracks to hide.
The data for older assemblies may be available on our Downloads page. Only a basic set of tracks appears initially in a new assembly. For specific information about the contributors of a given track, look at the Credits section on a track’s description page. Getting started on the Table Browser The Table Browser provides text-based access to the genome assemblies and annotation data stored in the Genome Browser database.
As a flexible alternative to the graphical-based Genome Browser, this tool offers an enhanced level of query support that includes restrictions based on field values, free-form SQL queries, and combined queries on multiple tables.
Output can be filtered to restrict the fields and lines returned, and may be organized into one of several formats, including a simple tab-delimited file that can be loaded into a spreadsheet or database as well as advanced formats that may be uploaded into the Genome Browser as custom annotation tracks. The Table Browser provides a convenient alternative to downloading and manipulating the entire genome and its massive data tracks. See the Downloading Genome Data section.
Getting started using Sessions The Sessions tool allows users to configure their browsers with specific track combinations, including custom tracks, and save the configuration options. Multiple sessions may be saved for future reference, for comparison of scenarios or for sharing with colleagues. Saved sessions persist for four months after the last access, unless deleted. User-generated tracks can be saved within sessions. This tool may be accessed by clicking the «My Data» pulldown in the top blue navigation bar in any assembly and then selecting Sessions.
Individual sessions may be designated by the user as either «shared» or «non-shared» to protect the privacy of confidential data. To avoid having a new shared session from someone else override existing Genome Browser settings, users are encouraged to open a new web-browser instance or to save existing settings in a session before loading a new shared session.
For more detailed information on using the Session tool, see the Sessions User Guide. The Genome Graphs tool can be used to display genome-wide data sets such as the results of genome-wide SNP association studies, linkage studies, and homozygosity mapping.
This tool is not pre-loaded with any sample data; instead, you can upload your own data for display by the tool. Once you have uploaded your data, you can view it in a variety of ways. You can view multiple sets of genome-wide data simultaneously either as superimposed graphs or side-by-side graphs.
Once you see an area of interest in the Genome Graphs view, you can click on it to go directly to the Genome Browser at that position. You can also set a significance threshold for your data and view only regions or gene sets that meet that threshold.
It enables the user to examine cell-by-cell as well as tissue-by-tissue expression patterns. The browser serves as a virtual microscope, allowing users to retrieve images that meet specific search criteria, then interactively zoom and scroll across the collection.
The search returns only those images that match all the specified criteria. For a list of sample search strings, see the VisiGene Gateway page. When searching on author names that include initials, use the format Smith AJ. Image Navigation Following a successful search, VisiGene displays a list of thumbnails of images matching the search criteria in the lefthand pane of the browser.
By default, the image corresponding to the first thumbnail in the list is displayed in the main image pane. If more than 25 images meet the search criteria, links at the bottom of the thumbnail pane allow the user to toggle among pages of search results. To display a different image in the main browser pane, click the thumbnail of the image you wish to view. By default, an image is displayed at a resolution that provides optimal viewing of the overall image.
This size varies among images. The image may be zoomed in or out, sized to match the resolution of the original image or best fit the image display window, and moved or scrolled in any direction to focus on areas of interest. The original full-sized image may also be downloaded. Zooming in: To enlarge the image by 2X, click the Zoom in button above the image or click on the image using the left mouse button.
Zooming out: To reduce the image by 2X, click the Zoom out button above the image or click on the image using the right mouse button. Alternatively, the – key may be used to zoom out when the main image pane is the active window.
Sizing to full resolution: Click the Zoom full button above the image to resize the image such that each pixel on the screen corresponds to a pixel in the digitized image. Sizing to best fit: Click the Zoom fit button above the image to zoom the image to the size that best fits the main image pane. Moving the image: To move the image viewing area in any direction, click and drag the image using the mouse.
Alternatively, the following keyboard shortcuts may be used after clicking on the image: Scroll left in the image: Left-arrow key or Home key Scroll right in the image: Right-arrow key or End key Scroll up in the image: Up-arrow key or PgUp key Scroll down in the image: Down-arrow key or PgDn key. Downloading the original full-sized image: Most images may be viewed in their original full-sized format by clicking the «download» link at the bottom of the image caption.
NOTE: due to the large size of some images, this action may take a long time and could potentially exceed the capabilities of some Internet browsers. If you have an image set you would like to contribute for display in the VisiGene Browser, contact Jim Kent.
The Genome Browser provides a feature to configure the retrieval, formatting, and coloring of the text used to depict the DNA sequence underlying the features in the displayed annotation tracks window. Retrieval options allow the user to add a padding of extra bases to the upstream or downstream end of the sequence.
Formatting options range from simply displaying exons in upper case to elaborately marking up a sequence according to multiple track data.
The DNA sequence covered by various tracks can be highlighted by case, underlining, bold or italic fonts, and color. The DNA display configuration feature can be useful to highlight features within a genomic sequence, point out overlaps between two types of features for example, known genes vs.
To display extra bases upstream of the 5′ end of your sequence or downstream of the 3′ end of the sequence, enter the number of bases in the corresponding text box. This option is useful in looking for regulatory regions. The Sequence Formatting section lists several options for adjusting the case of all or part of the DNA sequence.
To choose one of these formats, click the corresponding option button, then click the get DNA button. The page provides instructions for using the formatting table, as well as examples of its use. The list of tracks in the Track Name column is automatically generated from the list of tracks available on the current genome. Keep the formatting simple at first: it is easy to make a display that is pretty to look at but is also completely cryptic. Also, be careful when requesting complex formatting for a large chromosomal region: when all the HTML tags have been added to the output page, the file size may exceed the size limits that your internet browser, clipboard, and other software can safely display.
The maximum size of genome that can be formatted by the tool is approximately 10 Mbp. Converting data between assemblies Coordinates of features frequently change from one assembly to the next as gaps are closed, strand orientations are corrected, and duplications are reduced. Occasionally, a chunk of sequence may be moved to an entirely different chromosome as the map is refined.
There are three different methods available for migrating data from one assembly to another: BLAT alignment, coordinate conversion, and coordinate lifting. Coordinate conversion The Genome Browser Convert utility is useful for locating the position of a feature of interest in a different release of the same genome or in some cases in a genome assembly of another species. During the conversion process, portions of the genome in the coordinate range of the original assembly are aligned to the new assembly while preserving their order and orientation.
In general, it is easier to achieve successful conversions with shorter sequences. When coordinate conversion is available for an assembly, click on the «View» pulldown on the top blue menu bar on the Genome Browser page and select the «In Other Genomes Convert » link. Select the genome and assembly to which you’d like to convert the coordinates, then click the Submit button. If the conversion is successful, the browser will return a list of regions in the new assembly, along with the percent of bases and span covered by that region.
Click on a region to display it in the browser. If the conversion is unsuccessful, the utility returns a failure message. Lifting coordinates The liftOver tool is useful if you wish to convert a large number of coordinate ranges between assemblies. Web-based coordinate lifting To access the graphical version of the liftOver tool, click on «Tools» pulldown in the top blue menu bar of the Genome Browser, then select LiftOver from the menu. To convert one or more coordinate ranges using the default conversion settings: Select the genome and assembly from which the ranges were taken «Original» , as well as the genome and assembly to which the coordinates should be converted «New».
Enter coordinate ranges in the selected data format into the large text box, one per line. Click Submit. Alternatively, you may load the coordinate ranges from an existing data file by entering the file name in the upload box at the bottom of the screen, then clicking the Submit File button. The default parameter settings are recommended for general purpose use of the liftOver tool.
However, you may want to customize settings if you have several very large regions to convert. Command-line coordinate lifting The command-line version of liftOver offers the increased flexibility and performance gained by running the tool on your local server. This utility requires access to a Linux platform. The executable file may be downloaded here. Pre-generated files for a given assembly can be accessed from the assembly’s «LiftOver files» link on the Downloads page.
If the desired conversion file is not listed, send a request to the genome mailing list and we may be able to generate one for you. Downloading genome data Most of the underlying tables containing the genomic sequence and annotation data displayed in the Genome Browser can be downloaded.
This data was contributed by many researchers, as listed on the Genome Browser Credits page. Please acknowledge the contributor s of the data you use. Downloading the data Genome data can be downloaded in different ways: — Via rsync: The UCSC Genome Bioinformatics hgdownload site contains download directories for all genome versions currently accessible in the Genome Browser.
This download method is not recommended if you plan to download a large file or multiple files from a single directory compared to rsync see above. You can, however, use the mget command to download multiple files: mget filename1 filename2 , or mget -a to download all the files in the directory.
If the data you wish to download pre-dates the assembly versions listed, look for the data on our Downloads page. Types of data available There may be several download directories associated with each version of a genome assembly: the full data set bigZips , the full data set by chromosome chromosome , the annotation database tables database , and one or more sets of comparative cross-species alignments.
Depending on the genome, this directory may contain some or all of the following files: — chromAgp. Repeats from RepeatMasker and Tandem Repeats Finder are shown in lower case; non-repeating sequence is in upper case.
The main assembly is contained in the chrN. Repeats are masked by capital Ns; non-repeating sequence is shown in upper case. All contigs are in forward orientation relative to the chromosome. In some cases, this means that contigs will be reversed relative to their orientation in the NCBI assembly. Repeats are shown in lower case; non-repeating sequence is shown in upper case.
Repeats are masked by capital N s; non-repeating sequence is shown in upper case. This includes only cases where the transcription start is annotated separately from the coding region start. Chromosomes contains the assembled sequence for the genome in separate files for each chromosome in a zipped fasta format. The main assembly can be found in the chrN. Database contains all of the positional and non-positional tables in the genome annotation database.
Each table is represented by 2 files: Schema descriptions for all tables in the genome annotation database may be viewed by using the «describe table schema» button in the Table Browser. Cross-species alignments directories, such as the vsMm4 and humorMm3Rn3 directories in the hg16 assembly, contain pairwise and multiple species alignments and filtered alignment files used to produce cross-species annotations.
Creating custom annotation tracks The Genome Browser provides dozens of aligned annotation tracks that have been computed at UCSC or have been provided by outside collaborators. In addition to these standard tracks, it is also possible for users to upload their own annotation data for temporary display in the browser.
These custom annotation tracks are viewable only on the machine from which they were uploaded and are automatically discarded 48 hours after the last time they are accessed, unless they are saved in a Session. Optionally, users can make custom annotations viewable by others as well. Custom tracks are a wonderful tool for research scientists using the Genome Browser. Because space is limited in the Genome Browser track window, many excellent genome-wide tracks cannot be included in the standard set of tracks packaged with the browser.
Other tracks of interest may be excluded from distribution because the annotation track data is too specific to be of general interest or can’t be shared until journal publication.
Many individuals and labs have contributed custom tracks to the Genome Browser website for use by others. To view a list of these custom annotation tracks, click the Custom Tracks link on the Genome Browser home page. Custom annotation tracks are similar to standard tracks, but never become part of the MySQL genome database.
Each track has its own controller and persists even when not displayed in the Genome Browser window, e. Typically, custom annotation tracks are aligned under corresponding genomic sequence, but they can also be completely unrelated to the data.
For example, a track can be displayed under a long sequence consisting of millions of N s. Genome Browser annotation tracks are based on files in line-oriented format. Each line in the file defines a display characteristic for the track or defines a data item within the track. Annotation files contain three types of lines: browser lines, track lines, and data lines.
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