Help

This page provides help for the Splicing Graph Viewer (see methodology for the advantages of splicing graphs.)The screenshot below shows an example of the Splicing Graph Viewer (click here for a larger screenshot). Users first select a splicing graph that they are interested in via the query page or using the navigational aids. The users can then click on specific items in the splicing graph and transcripts to see detailed information in the "Detailed information" region. Alternatively users can opt to view information about the splicing graph by selecting an item from the "Detailed information menu".

There are 5 regions highlighted in yellow in the screenshot. Click on them for more information about that region.

Navigational aids

A close up of the navigational aids is shown below (click for a larger image). The button labeled "DEDB" brings the user back to the query page allowing the user to query the database using various methods. The next and previous buttons provide a means to browse the splicing graphs back and forth. The "Next AS" and "Previous AS" buttons allow users to jump to the next and previous alternative splicing graph quickly. Users can also use the selector to navigate to specific types of alternative splicing graphs by selecting a specific alternative splicing type and then clicking the "Go" button.

Splicing Graph

A close up of a splicing graph is shown below. Each of the black colored bars represent a node. Users can click the node to see detailed information on the node in the "Detailed Information" region. The green colored lines represents connections which linked nodes together. The Node ID is displayed in white numbers within the black bars. The start and stop codons are represented by green and red colored lines respectively within the nodes.

Transcripts

A close up of the transcript region is shown below. Each transcript that makes up the splicing graph is shown in this region. Each of the transcript is represented by a series of black colored bars representing the exons that are connected by introns represented by green lines. Both the exons and introns can be clicked to reveal more information in the "Detailed Information" region. On the top left of each transcript is the transcript name. In the middle of the intron is a number representing the intron phase. The start and stop codons like the splicing graph are represented by green and red lines respectively. The Pfam domains mapped onto the exons are displayed as colored bars below the transcript. Each Pfam domain can occur more than once in the transcript and this is reflected by the fact that these domains share the same color. Similar to the exons and introns, more information can be obtained by clicking on the domain.

Detailed information menu

The detailed information menu provides a means to display specific information concerning the splicing graph. The information will be displayed just below the menu in the "Detailed Information" region. The details of each button is provided below:

• Synonyms
  This provides a list of all the gene synonyms associated with this splicing graph.
• FlyBase Links
  Links to FlyBase are provided when users click on this button. Click here for more information.
• GO
  Users can view the Gene Onotology information available for this splicing graph by clicking on this button.
• Node Summary
  This provides a table of all the nodes contained in this splicing graph. The Node ID is clickable resulting in detailed information about the node. This has the same effect as clicking on the node in the splicing graph region.
• Exon Summary
  Similar the Node Summary, the Exon Summary provides tables that list all the exons found in the splicing graph. As with the Node Summary, clicking on the Exon ID results in detailed information about the exon. This has the same effect as clicking on the exon in the transcript region.
• Sequence Summary
  The Sequence Summary provides a table that list all the transcripts used to construct the splicing graph. Information on the strand, exons, nodes, translation start and translation stop are provided. Users can download FASTA formatted sequences of these transcripts by clicking on the "FASTA Download" button found at the end of each row.
• Alternative Splicing Summary
  This provides a table showing the various alternative splicing events that occur.
• Domains Summary
  This provides a table showing the various Pfam domains mapped onto the transcripts. Detailed information about each Pfam domain can be obtained by clicking on the Model name.

Detailed information

This region provides space for detailed information about selected items. For items with sequence information, a "Download FASTA sequence" button will appear. Click on this button to open a new page with the FASTA sequence of the item in question.