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GQ Gene Viewer
GQ Gene consists of GQ Gene Database and GQ Gene Viewer. GQ Gene Database is a database of gene-related information mapped on to the sequence of the transcribed portion of the gene. Gene-related sequences outside of the transcribed portion (like regulatory elements which are upstream of the transcription start site or those downstream of the transcription end site) are not included in the sequence. Various other pieces of information are pre-mapped on to the genes including:
- RefSeq transcripts – mapped to the gene using coordinates from Entrez Gene.
- GenBank transcripts – mapped by GenomeQuest using a spliced alignment algorithm (Splign*).
- Single Nucleotide Polymorphisms – mapped to the gene using coordinates from dbSNP at NCBI.
- A set of GenBank ESTs selected by Server – mapped by GenomeQuest using the Splign* alignment algorithm.
- Agilent microarray Probes.
Apart from this pre-mapped information, a number of query and uploaded sequences can be mapped on the fly to the gene through a simple sequence search, which will be explained later.
GQ Gene Viewer allows users to view all the mapped information in an interactive browser. Section 1.1 to 1.6 details the way to view, add, and manipulate the data in the viewer. The probe selection process is explained in section 1.7.
Searching the GQ Gene Database
Browse the GQ Gene Database to look up general information on a gene or to launch the viewer. The way to browse this database is to the run an annotation search on it as explained in the sequence search help page. GQ Gene Databases are created on a per-organism basis. To see which organisms are currently covered, expand the GQ Gene node on the database tree (Fig 1).
Fig 1. Genomequest Sequence Search page.
GQ Gene Database can also be searched using query sequence(s). To do this, follow the steps in the Sequence Search section. When a query sequence(s) searched against any GQ Gene Database, the query sequence(s) are mapped to the genes on the fly. This allows you to see the query sequences in the context of the other public sequences when the viewer is opened. Note: GQ Gene databases are displayed on the Nucleotide side. If you do not see these databases, it may be because proper access permissions have not been enabled; contact your GenomeQuest Administrator or firstname.lastname@example.org to request permissions.
Launching GQ Gene Viewer
You can launch the GQ Gene Viewer to see all mappings to a gene. To launch GQ Gene Viewer when browsing a GQ Gene Database, simply click on the “Gene View” link of any gene (Fig 2).
Fig 2. GQ Gene entries.
The “Gene View” link is also available from the results of a sequence search if the subject sequence is from a GQ Gene Database. Just open the Subject Annotation tab of the subject record (Fig 3).
Fig 3. Result Browser page.
If the viewer fails to launch, please see our troubleshooting page.
GQ Gene Viewer consists of a number of informational panes (Fig 4). The presence or absence of each of these panes can be controlled interactively. The main viewing area is numbered 4 in Fig 4, and it shows the mapping of public domain (Refseq and GenBank) transcripts to the gene. The other areas are briefly described in the caption under Fig 4.
Fig 4. GQ Gene Viewer in default mode, and launched from an Annotation search page. (1) The top level Menu Bar; (2) An informational area about the gene currently being viewed; (3) The transcript list area from where transcript lists can be manipulated. (4) The public transcript mapping area which shows how public domain transcripts from Refseq and GenBank map to the gene. (5) The microarray probe area showing how agilent probes map to the gene. At the bottom of the Console (6), general information about the gene as well as the various selections made interactively are displayed.
In this main viewing area, you can select or unselect displayed transcripts. Operations from the menu bar generally apply to the selected transcripts. To select a transcript, click on its identifier. Then, you will see the transcript get highlighted. To unselect a selected transcript, click on the highlighted transcript. Your selections (and unselections) are printed to the Console area as shown in Fig 5.
The gene is shown fully; i.e. from end to end when it is first opened. However, you can zoom into specific portions of the gene using the zooming bar (Fig 6). The red box around the gene map area shows the portion of the gene that is currently being viewed.
To view a smaller portion (to zoom), point the mouse to the black dots at the ends of the view box and drag them in (Fig 6).
To navigate around the gene, place your mouse within the view box and drag to the left or right (Fig 8).
Controling Viewable Features
Directly below the view box are the following checkboxes.
- Show Sequences – This checkbox zooms to the maximum level possible and displays the actual bases (sequences) of the gene as well as other features. In sequence mode, you will see highlighting of bases when the match to the gene sequence is not perfect.
- Show Proteins – Where available, this checkbox also displays the protein sequences translated from the different Open Reading Frames.
- Show Introns – This box is checked by default. When unchecked the introns are removed from view so that exons may be examined in greater detail.
- Show SNPs – This checkbox controls whether single nucleotide polymorphisms from dbSNP are displayed in the gene.
Menu Bar Items
- The Export menu allows you to export sequences of transcripts.
- Fasta – nuc : exports the nucleotide sequences of the selected transcripts.
- Fasta – Prot : exports the protein sequences (translated from the annotated open reading frame) of the selected transcripts.
- Pictures : creates and exports GIF pictures of the panes in the viewer.
- The Applications menu allows you to launch applications which are not native to GenomeQuest. Currently the ClustalW application is available. ClustalW can be run on the nucleotide or protein sequences of the selected transcripts.
- The View menu controls what is viewed in the screen.
- Remove Selected Transcripts : removes the selected transcripts from view and redraws the viewer. This is useful when you want to remove from view particular transcripts with an exon-intron structure that is very different from others. These transcripts are moved under the "Ignored Transcripts" list in the List area.
- Restore Transcripts : in order to bring “removed” transcripts back into the view, select them from the ignored transcripts list and choose this option.
- Restore All Transcripts : this option brings you back to the default mode showing all transcripts from Refseq and GenBank.
- Full Frame : When this option is checked, the list area disappears from display and the main viewing area expands to give a more detailed view.
- Show Panels : controls which panels are shown in the display.
- Themes : allows you to control the colors of the exons, introns, and other features.
- The Help menu has links to the following documentation:
- "GQ Gene Help" : this brings you to this documentation.
- "Show Log" : this shows the log of operations done in GQ Gene Viewer up to this point, which is useful for troubleshooting.
- "About GQ Gene" : this displays the version number and credits for GQ Gene.
Mapping Your Own Data
A GQ Gene Database(s) can be searched using a query sequence(s). To do this, follow the steps in the Sequence Search section. When a query sequence is searched against a GQ Gene Database(s), the query sequence(s) is aligned to a genomic region that contains the gene for which it was aligned to. When the genome viewer is opened, you can see the query sequence(s) mapped to a gene, and in the context of the other public sequences such as GenBank mRNAs and ESTs that are displayed. Note: GQ Gene databases are displayed on the Nucleotide side. If you do not see these databases, it may be because the proper access permissions have not been enabled; contact your GenomeQuest Administrator or email@example.com to request permissions.
Opening the GQ Gene Viewer with your results
When browsing your results, if your query sequence(s) is mapped to a GQ Gene Database subject sequence, you will see a "gene name" column in the display. This field contains the gene name info and the "Gene View" link (Fig 13).
Fig 13. Result Browser page.
Clicking this link allows you to launch the GQ Gene Viewer with all gene components and your hit(s).
Looking at your results
When the Viewer is opened you can see that a "Hits" pane has been added(Fig 14).
Fig 14. GQ Gene Viewer dislpaying hits.
Each pane or each molecule type has specific features that can be used from each tab menu in the title bar.
Fig 15. Pane menus.
- SNPs: Fetching SNPs from the NCBI dbSNP database. Then SNPs are visible under the genomic sequence. Available for Human genes only (Fig 16).
- Sort by: Allows you to sort transcripts according to different criteria such as DB sources or CDS start positions (Fig 17).
- Proteins: Available when you are at the sequence level. This adds protein sequences contained in tracks (Fig 18.a).
- Consensus: Displays a symbol line (Fig 18.b) representing the nucleotide consensus of all transcripts at a given position.
- Compress Hits: Compress the view(Fig 19)
- Tracks: Show/Hide hit tacks.
- Consensus: Show/Hide Hit consensus pane (Fig 20.c)
- Putative SNPs: Open a tool bar (Fig 20.a) under the title. This allows you to browse hit variations.
- Coverage: Show/Hide Hit coverage pane(Fig 20.b)