GBrowse0.5 & GBrowse3.1(on SpBase)

GBrowse0.5 & GBrowse3.1 display genomic features for Strongylocentrotus purpuratus genome assembly version 0.5 and version 3.1. We use GBrowse, an open-source genome browser by GMOD

General Help (from GBrowse user guide)

To quickly learning how to navigate your way around GBrowse, watch this video tutorial: http://www.openhelix.com/gbrowse

Notes on using GBrowse

To select a region of the genome to view, enter its name in the text field labeled "Landmark or Region". For Sea Urchin assembly you can search by gene name, SPU ID, transcriptome ID/WHL IDs, BAC-end, contig, eBAC, EST or even structural landmarks such as Scaffold. If the landmark is found in the database, the browser will display the region of the genome that covers it. The region is displayed in three graphical panels:

overview panel: This panel displays the genomic context, a large portion of the sequence assembly such as a scaffold in our case. A highlighted rectangle indicates the region of the genome that is displayed in the detail panel and corresponds to the region found when you search for a gene or other feature. This rectangle may appear as a single line if the detailed region is relatively small.

region panel: This panel displays a portion of the genome surrounding the region of interest. It gives the context for the search region.

detail panel: This panel displays a zoomed-in view of the genome corresponding to the overview's selection rectangle. The detail panel consists of one or more tracks showing annotations and other features that have been placed on the genome. The detail panel is described at length later in the GBrowse3.1 section

Viewing a Precise Region around a Landmark

You can view a precise region around a landmark using the notation landmark:start..stop, where start and stop are the start and stop positions of the sequence relative to the landmark. The beginning of the feature is position 1. For example, to view first 20kb on Scaffold 1 use following search notation: scaffold1:1..2,000 This offset notation will work correctly for negative strand features as well as positive strand features. The coordinates are always relative to the feature itself.

Searching for Keywords and Multiple Hits

Anything that you type into the "Landmark or Region" textbox that isn't recognized as the name of a landmark will be treated as a full text search across the feature database. This will find comments or other feature notations that match the typed text. If more than one landmark or keyword search is found, then the browser will display a graphical representation of the whole genome and summarize the various hits in a table. You can click on one of the landmarks in either the graphical display or the table in order to view it in the detail view. Example: SPU_018921.

Once a region is displayed, you can navigate through it in a number of ways:
1. Click and drag on any of the rulers
Any of the rulers that show base position, including those in the overview, region and detail panels, are clickable. Click once to recenter the view at the desired position, or click and drag to select a region.

2. Scroll left or right with the and >> buttons
These buttons, which appear in the "Scroll/Zoom" section of the screen, and at the top right and left corners of the detail panel, will scroll the detail panel to the left or right. The > buttons scroll an entire screen's worth, while > scroll a half screen.

3. Zoom in or out using the "Show XXX Kbp" menu.
Use menu that appears in the center of the "Scroll/Zoom" section to change the zoom level. The menu item name indicates the number of base pairs to show in the detail panel. For example, selecting the item "100 Kbp" will zoom the detail panel so as to show a region 100 Kbp wide.

4. Make fine adjustments on the zoom level using the "-" and "+" buttons.
Press the - and + buttons to change the zoom level by small increments

5. Flip the orientation by selecting the "flip" checkbox
To flip the browser display so that the minus strand points to the right, select the "flip" checkbox. This is sometimes useful for looking at minus strand genes.

6. Recenter the detail panel by clicking on its scale
The scale at the top of the detail panel is live. Clicking on it will recenter the detail panel around the location you clicked. This is a fast and easy way to make fine adjustments in the displayed region.

7. Mouse over a feature to get more information about it
Mousing over a feature will usually bring up a text bubble that contains more identifying information about the feature.

8. Click on a feature to see its details
Clicking on a feature in the detail view will link to a page that displays detailed information on it. This is a page on the browser's web site.

The Detail Panel

The detailed view is composed of a number of distinct tracks which stretch horizontally from one end of the display to another. Each track corresponds to a different type of genomic feature, and is distinguished by a distinctive graphical shape and color.
Each track has a descriptive name printed above it, and a series of small control icons to the left of the name.
1. To reorder a track, click on its name and drag it up or down to the desired position.
2. To minimize a track, click on its "-" icon. The track will minimize down to the name only and the icon will change to a "+". Click on the icon again to maximize the track.
3. To turn off a track, click on its "x" icon. The track will disappear entirely, but can be reenabled by selecting its name in the track table described below.
4. To share a track such that the track data can be imported into another instance of the browser, click on the icon that looks like a set of radio waves (. This will pop up a window containing a link that you can cut and paste into another instance of the Generic Genome Browser)
5. To get more information about track, mouse over its "?" icon. This will bring up any descriptive information that the site administrator has provided for the track.
6. To change a track's appearance, click on the "?" icon. This will present you with a pop-up window that allows you to change many aspects of the track, including its height, display style, and color.

Uploading Your Own and 3d Party Annotations

This browser supports uploading your own data set tracks. You can then share these tracks with other individuals and groups.

Entering New Data Sets

To upload a custom track to the browser, click on the link labeled "Upload and Share Tracks" located towards the top of the screen. This will open a new text editing area. Type in one or more lines of genomic feature information following the example in the screenshot below. The simplest upload format is called BED, and takes three space-separated fields:

Where is the name of the Scaffold that the feature lives on, and and indicates the range that the feature spans. (The BED format uses zero-based coordinates, so the first base of the chromosome is actually position 0. Other formats accepted by GBrowse use the more familiar one-base coordinates.).

Press the "Upload" button. The indicated features will be uploaded to GBrowse and information about the upload set will be displayed in a new section similar to this one:

To view your uploaded annotations in a new browser track, click on the "View track" link. Note that you may need to navigate to the region of the genome containing the annotations in order to see them. To edit the annotations, click the "edit" link to the right of the name of the upload file (in this example "upload_4787").

To customize the appearance of the track, press the "edit" link to the right of the "Configuration" line. Note that this involves editing a configuration file that has many options. You can perform all basic customization tasks such as changing the height and color of your uploaded features, much more conveniently by clicking the "?" icon next to the track itself.

To add a description to the uploaded set, click on the line that reads "Click to add a description" and type in a one-line description of the data. Press the escape key to undo the changes. Press return or mouse out of the description area to accept the change.

To delete the uploaded annotation data completely, click the trash can icon.

To share an uploaded track with another person, go to the main browser tab

GBrowse3.1

Assembly contig

This track shows the position of a contig within the scaffold. A contig is continuous sequence of DNA that has been assembled from overlapping cloned DNA fragments. It may include draft and finished sequence. It may contain sequence gaps (within a clone), but it does not include gaps between clones (http://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/).

eBACs

This track displays the position of the deconvoluted individual BAC sequences enriched with WGS sequences. These sequences were generated during the genome sequencing project using pools of arrayed BACs from a whole genome tiling path.

BAC-END

This track shows the location and coordinates of the sequenced ends of clones from the sperm genomic BAC library. These sequences provided the first virtual map of the genome (http://www.spbase.org/SpBase/resources/index.php).

EST

This track shows the position of expressed sequence tags (EST) in the genome. An EST is a short sub-sequence of a transcribed cDNA sequence produced by one-shot sequencing of a cloned mRNA.

GLEAN-UTR:Prediction

This track shows the location and coordinates of predicted genes based on the Spur0.5 genome assembly (Sodergren ref). GLEAN refers to a program that combined data from several diverse predictive methods (ab initio, homology-based or empirical) to reach a consensus prediction. The consensus gene-set contains 28,944 unique genes. The added UTR predictions were identified form a whole genome tiling array hybridized with embryo mRNA (samanta science ref). SpBase converted those 28,944 GLEAN identifiers to SPU numbers by adding a zero and changing the prefix; GLEAN3_00001 is the same as SPU_000001 SPU identifiers over SPU_030000 denote gene sequences derived from other sources than the predicted set.
You can visualize 3'UTR for GLEAN gene, a vertical line separates the gene with 3'UTR

Transcriptome

This track shows the position and structure of expressed gene sequences read from cDNA samples collected from 10 different embryonic stages, 6 feeding larval and metamorphosed juvenile stages, and 6 adult tissues. The reads were produced in the Illumina sequencing machine using a paired-end strategy and assembled using the Bowtie-TopHat-Cufflink software package.

Transcriptome Read Coverage

This track shows an X-Y plot of the coverage of the 621 million transcriptome reads mapped to the genome.

Lytechinus variegatus

This track shows the position of conserved non-coding sequence patches between the S. purpuratus genome and the L. variegatus genome. These two genomes shared a common ancestor 50 million years ago. In the time since divergence only the function sequences are likely to remain as the rest changes due to genetic drift and small insertions and deletions.

AF reads

This track shows the position of Roche 454 reads from Allocentrotus fragilis (AF) mapped to the S. purpuratus genome. This comparison conforms to a rule that modestly distant species comparisons reveal regulatory modules because large indels (>20 bp) are statistically almost absent within the regulatory modules, although they are common in flanking intergenic or intronic sequence.

Sf reads

This track shows the position of Roche 454 reads from Strongylocentrotus franciscanus (SF) mapped to the S. purpuratus genome. This comparison conforms to a rule that modestly distant species comparisons reveal regulatory modules because large indels (>20 bp) are statistically almost absent within the regulatory modules, although they are common in flanking intergenic or intronic sequence.

Feature Details

Click on a feature to see its details. Clicking on a feature in the detail view will link to a page that displays detailed information on it. This is a page on the browser's web site.

Figure: Clicking on feature (in this case transcriptome WHL22.241462.0) would direct you to feature detail page

Figure: Feature detail page for transcriptome WHL22.241462.0