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. The Get DNA in Window page that appears contains sections for configuring the retrieval and output format.
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, a Convert link is displayed in the top menu bar on the Genome Browser tracks page.
Click this link to convert the currently-displayed coordinate range. 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 the Utilities link in the left-hand sidebar on the Genome Browser home page, then select the Batch Coordinate Conversion liftOver link. 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 two different ways: -- Via ftp: The UCSC Genome Bioinformatics ftp site contains download directories for all genome versions currently accessible in the Genome Browser.
This download method is recommended if you plan to download a large file or multiple files from a single directory. 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 in the archives accessible from the Archive link on the home 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. Empty lines and those starting with " " are ignored. To construct an annotation file and display it in the Genome Browser, follow these steps: Step 1.
Format the data set Formulate your data set as a tab-separated file using one of the formats supported by the Genome Browser. Chromosome references must be of the form chrN the parsing of chromosome names is case-sensitive. You may include more than one data set in your annotation file; these need not be in the same format. Step 2. Define the Genome Browser display characteristics Add one or more optional browser lines to the beginning of your formatted data file to configure the overall display of the Genome Browser when it initially shows your annotation data.
Browser lines allow you to configure such things as the genome position that the Genome Browser will initially open to, the width of the display, and the configuration of the other annotation tracks that are shown or hidden in the initial display.
NOTE: If the browser position is not explicitly set in the annotation file, the initial display will default to the position setting most recently used by the user, which may not be an appropriate position for viewing the annotation track. Step 3.
Define the annotation track display characteristics Following the browser lines--and immediately preceding the formatted data--add a track line to define the display attributes for your annotation data set.
Track lines enable you to define annotation track characteristics such as the name, description, colors, initial display mode, use score, etc. If you have included more than one data set in your annotation file, insert a track line at the beginning of each new set of data.
Example 1: Here is an example of a simple annotation file that contains a list of chromosome coordinates. Example 2: Here is an example of an annotation file that defines 2 separate annotation tracks in BED format. The first track displays blue one-base tick marks every bases on chr The second track displays red base features alternating with blank space in the same region of chr Example 3: This example shows an annotation file containing one data set in BED format.
The track displays features with multiple blocks, a thick end and thin end, and hatch marks indicating the direction of transcription. The track labels display in green 0,,0 , and the gray level of the each feature reflects the score value of that line. NOTE: The track name line in this example has been split over 2 lines for documentation purposes. If you paste this example into the Genome Browser, you must remove the line break to display the track successfully.
Click here for a copy of this example that can be pasted into the browser without editing. Step 4. Download the bedGraphToBigWig program from the directory of binary utilities. Because the bigWig files are indexed binary files, they can be difficult to extract data from. Consequently, we have developed the following two programs, both of which are available from the directory of binary utilities.
As with all UCSC Genome Browser programs, simply type the program name at the command line with no parameters to see the usage statement. Example One In this example, you will use an existing bigWig file to create a bigWig custom track. Example Two In this example, you will create your own bigWig file from an existing wiggle file. Example Three To create a bigWig track from a bedGraph file, follow these steps: Create a bedGraph format file following the directions here.
Extracting Data from the bigWig Format Because the bigWig files are indexed binary files, they can be difficult to extract data from. In some cases, bigWigSummary and bigWigAverageOverBed will produce very similar results, but in other cases, the results may differ. This is due to differences in how the utilities handle data.
Summary levels are used with bigWigSummary, so some rounding errors and border conditions are encountered when extracting data over relatively small regions. Cath Tyner. UCSC hg38 datasets. Vorechovsky I. Reply to author. Report message as abuse.
Show original message. Either email addresses are anonymous for this group or you need the view member email addresses permission to view the original message. Thank you. Hello Dr. Our support team has identified various approaches which can assist you, but I would first like to clarify your question so that we can provide the best method. I believe that the query described above included annotations for all transcripts.
As there are multiple transcripts per gene due to alternative splicing, etc. UCSC's other major roles include building genome assemblies, creating the Genome Browser work environment, and serving it online.
The majority of the sequence data, annotation tracks, and even software are in the public domain and are available for anyone to download. Read more. Table Browser - convenient text-based access to the database underlying the Genome Browser.
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. Gene Sorter - expression, homology, and other information on groups of genes that can be related in many ways. To get started, click the Browser link on the blue sidebar. This will take you to a Gateway page where you can select which genome to display. Note that there is also an official European mirror site for users who are geographically closer to central Europe than to the western United States.
Opening the Genome Browser at a specific position To get oriented in using the Genome Browser, try viewing a gene or region of the genome with which you are already familiar, or use the default position. To open the Genome Browser window: 1.
Select the clade, genome and assembly that you wish to display from the corresponding pull-down menus. Assemblies are typically named by the first three characters of an organism's genus and species names. For older assemblies that are no longer available from the menu, the data may still be available on our Downloads page. Specify the genome location you'd like the Genome Browser to open to. To select a location, enter a valid position query in the search term text box at the top of the Gateway page or accept the default position already displayed.
The search supports several different types of queries : gene symbols, mRNA or EST accession numbers, chromosome bands, descriptive terms likely to occur in GenBank text, or specific chromosomal ranges. Click the submit button to open up the Genome Browser window to the requested location. In cases where a specific term accession, gene name, etc. Occasionally the Gateway page returns a list of several matches in response to a search, rather than immediately displaying the Genome Browser window.
When this occurs, click on the item in which you're interested and the Genome Browser will open to that location. The search mechanism is not a site-wide search engine. However, some types of queries will return an error, e. If your initial query is unsuccessful, try entering a different related term that may produce the same location. For example, if a query on a gene symbol produces no results, try entering an mRNA accession, gene ID number, or descriptive words associated with the gene.
Finding a genome location using BLAT If you have genomic, mRNA, or protein sequence, but don't know the name or the location to which it maps in the genome, the BLAT tool will rapidly locate the position by homology alignment, provided that the region has been sequenced. This search will find close members of the gene family, as well as assembly duplication artifacts.
An entire set of query sequences 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 input sequence. To view one of the alignments in the Genome Browser, click the browser link for the match.
The details link can be used to preview the alignment to determine if it is of sufficient match quality to merit viewing in the Genome Browser. Opening the Genome Browser with a custom annotation track You can open the Genome Browser window with a custom annotation track displayed by using the Add Custom Tracks feature available from the gateway and annotation tracks pages.
For more information on creating and using custom annotation tracks, refer to the Creating custom annotation tracks section.
Annotation track data can be entered in one of three ways: -- Enter the file name for an annotation track source file in the Annotation File text box. Once you've entered the annotation information, click the submit button at the top of the Gateway page to open up the Genome Browser with the annotation track displayed. The Genome Browser also provides a collection of custom annotation tracks contributed by the UCSC Genome Bioinformatics group and the research community.
NOTE: If an annotation track does not display correctly when you attempt to upload it, you may need to reset the Genome Browser to its default settings, then reload the track. For information on troubleshooting display problems with custom annotation tracks, refer to the troubleshooting section in the Creating custom annotation tracks section.
Viewing genome data as text The Table Browser , a portal to the underlying open source MySQL relational database driving the Genome Browser, displays genomic data as columns of text rather than as graphical tracks. Opening the Genome Browser from external gateways Several external gateways provide direct links into the Genome Browser.
Journal articles can also link to the browser and provide custom tracks. Be sure to use the assembly date appropriate to the provided coordinates when using data from a journal source. Tips for Use To facilitate your return to regions of interest within the Genome Browser, save the coordinate range or bookmark the page of displays that you plan to revisit or wish to share with others.
It is usually best to work with the most recent assembly even though a full set of tracks might not yet be ready. Be aware that the coordinates of a given feature on an unfinished chromosome may change from one assembly to the next as gaps are filled, artifactual duplications are reduced, and strand orientations are corrected. The Genome Browser offers multiple tools that can correctly convert coordinates between different assembly releases. For more information on conversion tools, see the section Converting data between assemblies.
To ensure uninterrupted browser services for your research during UCSC server maintenance and power outages, bookmark a mirror site that replicates the UCSC genome browser. 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 regions that are intrinsically difficult to sequence.
Artifactual duplications arise as unavoidable compromises during a build, causing misleading matches in genome coordinates found by alignment. Interpreting and fine-tuning the Genome Browser display The Genome Browser annotation tracks page displays a genome location specified through a Gateway search, a BLAT search, or an uploaded custom annotation track. There are five main features on this page: a set of navigation controls , a chromosome ideogram, the annotations tracks image, display configuration buttons , and a set of track display controls.
The first time you open the Genome Browser, it will use the application default values to configure the 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 of the 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 default settings, click the "Click here to reset" link on the Genome Browser Gateway page. To return the 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 page. Display conventions The annotation tracks displayed in the Genome Browser use a common set of display conventions: -- Annotation track descriptions: Each annotation track has an associated description page that contains a discussion of the track, the methods used to create the annotation, the data sources and credits for the track, and in some cases filter and configuration options to fine-tune the information displayed in the track.
To view the description page, click on the mini-button to the left of a displayed track or on the label for the track in the Track Controls section. The information contained in the details page varies by annotation track, but may include basic position information about the item, related links to outside sites and databases, links to genomic alignments, or links to corresponding mRNA, genomic, and protein sequences.
The 5' and 3' untranslated regions UTRs are displayed as thinner blocks on the leading and trailing ends of the aligning regions.
In full display mode, arrowheads on the connecting intron lines indicate the direction of transcription. In situations where no intron is visible e. In dense display mode, the degree of darkness corresponds to the number of features aligning to the region or the degree of quality of the match. In pack or full display mode, the aligning regions are connected by lines representing gaps in the alignment typically spliced-out introns , with arrowheads indicating the orientation of the alignment, pointing right if the query sequence was aligned to the forward strand of the genome and left if aligned to the reverse strand.
Two parallel lines are drawn over double-sided alignment gaps, which skip over unalignable sequence in both target and query. For alignments of ESTs, the arrows may be reversed to show the apparent direction of transcription deduced from splice junction sequences. In situations where no gap lines are visible, the arrowheads are displayed on the block itself. To prevent display problems, the Genome Browser imposes an upper limit on the number of alignments that can be viewed simultaneously within the tracks image.
When this limit is exceeded, the Browser displays the best several hundred alignments in a condensed display mode, then lists the number of undisplayed alignments in the last row of the track.
In this situation, try zooming in to display more entries or to return the track to full display mode. For some PSL tracks, extra coloring to indicate mismatching bases and query-only gaps may be available.
The boxes represent aligning regions. Single lines indicate gaps that are largely due to a deletion in the genome of the first species or an insertion in the genome of the second species. Double lines represent more complex gaps that involve substantial sequence in both species. This may result from inversions, overlapping deletions, an abundance of local mutation, or an unsequenced gap in one species. In cases where there are multiple chains over a particular portion of the genome, chains with single-lined gaps are often due to processed pseudogenes, while chains with double-lined gaps are more often due to paralogs and unprocessed pseudogenes.
In the fuller display modes, the individual feature names indicate the chromosome, strand, and location in thousands of the match for each matching alignment. Clicking on a box displays detailed information about the chain as a whole, while clicking on a line shows information on the gap. The detailed information is useful in determining the cause of the gap or, for lower level chains, the genomic rearrangement.
Individual items in the display are categorized as one of four types other than gap : Top - The best, longest match. Displayed on level 1. Multiple alignments of 4 vertebrate genomes with Fugu Conservation scores for alignments of 4 vertebrate genomes with Fugu.
Multiple alignments of 11 vertebrate genomes with Gorilla Conservation scores for alignments of 11 vertebrate genomes with Gorilla. Multiple alignments of 6 genomes with Lamprey Conservation scores for alignments of 6 genomes with Lamprey.
Multiple alignments of 5 genomes with Lamprey Conservation scores for alignments of 5 genomes with Lamprey. Multiple alignments of 4 genomes with Lancelet Conservation scores for alignments of 4 genomes with Lancelet.
Multiple alignments of 5 vertebrate genomes with Malayan flying lemur Conservation scores for alignments of 5 vertebrate genomes with Malyan flying lemur. Multiple alignments of 8 vertebrate genomes with Marmoset Conservation scores for alignments of 8 vertebrate genomes with Marmoset.
Multiple alignments of 4 vertebrate genomes with Medaka Conservation scores for alignments of 4 vertebrate genomes with Medaka. Multiple alignments of 6 vertebrate genomes with the Medium ground finch Conservation scores for alignments of 6 vertebrate genomes with the Medium ground finch Basewise conservation scores phyloP of 6 vertebrate genomes with the Medium ground finch.
Multiple alignments of 59 vertebrate genomes with Mouse Conservation scores for alignments of 59 vertebrate genomes with Mouse Basewise conservation scores phyloP of 59 vertebrate genomes with Mouse FASTA alignments of 59 vertebrate genomes with Mouse for CDS regions. GRCm38 Patch 6 - Sequence files. Multiple alignments of 29 vertebrate genomes with Mouse Conservation scores for alignments of 29 vertebrate genomes with Mouse Basewise conservation scores phyloP of 29 vertebrate genomes with Mouse FASTA alignments of 29 vertebrate genomes with Mouse for CDS regions.
Multiple alignments of 16 vertebrate genomes with Mouse Conservation scores for alignments of 16 vertebrate genomes with Mouse. Multiple alignments of 9 vertebrate genomes with Mouse Conservation scores for alignments of 9 vertebrate genomes with Mouse. Multiple alignments of 4 vertebrate genomes with Mouse Conservation scores for alignments of 4 vertebrate genomes with Mouse. Multiple alignments of 8 vertebrate genomes with Opossum Conservation scores for alignments of 8 vertebrate genomes with Opossum.
Multiple alignments of 6 vertebrate genomes with Opossum Conservation scores for alignments of 6 vertebrate genomes with Opossum.
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