III. Viewers
Two viewers are provided that show the transcript splice model for genomic sequences (Exon Viewer) and the position of protein domains for both genomic-based and transcript-based sequences (Pfam Domain Viewer and SMART Domain Viewer).
A. Exon Viewer:
This viewer is applicable for genomic-based organisms only.
Step 1. Starting the process; choose the organism(s)
a. Option 1: Manual entry of gene names
"Enter gene names” is a link that brings up a new page with a text box for manual entry of ChromDB IDs or loci (if available).
Note: Because a ChromDB ID has the protein group and organism encoded in the ID (see Nomenclature Link for more information); this selection does not use Step 2 which appears on the opening page of “Genomic-based Reports”.
b. Option 2: Selection of organisms from a list
All current genomic-based organisms are listed in the box in Step 1 of the opening page of “Genomic-based Reports”. Use this selection to access a single organism or to select multiple organisms (hold the control key while making multiple selections). Within the text box it is possible to jump to a selection by beginning to type in a name.
Note:The speed of the report generator is decreased with increased numbers of selections. Please be patient.
Step 2. Selection of protein classes
a. Option 1: Functional classification of protein groups
To understand the groupings, open the plus signs see the individual groups; the final enlargement of each group has the name and a short description of each ChromDB protein group.
b. Option 2: Alphabetical listing of protein groups
Each protein group includes a three to five letter abbreviation followed by a short description of the group. To make multiple selections, please hold down the control key while clicking on groups. Within the text box it is possible to jump to an abbreviation by beginning to type in the name.
Press “go” to view the selections
B. Protein Domain Viewer:
This viewer will generate a view of the placement of either Pfam or SMART domains within a predicted protein sequence. There are three different options, or entry points, associated with this feature.
1. Starting the process.
a. Option 1: Search by a list of gene/protein names.
The first sentence on the Advanced Search page, “Select both the taxon and protein classification or "Enter gene names”, contains the Option 1 link that brings up a new page with a text box and three types of information retrieval: Protein Description, Synonyms, and Protein Domain Viewer (these subjects are explained on the Advanced Search Page; click on a subject to jump to the description)
The text box accepts multiple entries as ChromDB IDs or loci (use the Synonyms link under the Reports section on the left side style sheet to see which organisms have loci associated with genes in the database. Go to Synonyms help for more information.)
Note: Because a ChromDB ID has the protein group and organism encoded in the ID (see Nomenclature Link for more information) and a locus is specific for an organism and gene/protein; this option does not require selections for the organism or a protein group (Steps 2 and 3, respectively, which appear on the opening page of the Advanced Search Utility).
Note: When using Option1, the "Make other selections" link at the top of the new page returns you to the original menu.
b. Option 2: Customize your organism selection from a list
Use the opening page selection to access a single organism or to customize a combination of organisms (hold the control key while making multiple selections). It is possible to jump within the text box to a selection by typing in a name.
Note:This search option requires the use of formal names for organisms. If you do not know the formal names, use the Quick Search text box to enter a common name in order to retrieve the formal name.
c. Option 3: Search by taxon criteria using pre-set groups of organisms
An alternative to selecting a group of organisms from the list is to "Select Taxon" link in Step one. This method provides the means to carry out a comparative analysis of a group or groups of organisms. The taxon groups are pre-set and cannot be altered. Each taxon name is a link to view the organisms within that group. The rest of the page continues the menu selection for Step 2 which selects a protein group (explained below) and Step 3 for data selection; Protein Description, Synonyms, and Protein Domain Viewer (these subjects are explained on the Advanced Search Page; click on a subject to jump to the description)
2. Step 2: Select a protein group or a domain
a. Option 1: Select a protein group from a list
This option provides an alphabetical listing of protein groups. Multiple choices can be made by holding down the control key.
b. Option 2: View by domain
Select Domains in Step 2 is a link to generate a report by domain, either Pfam or SMART, rather than by protein group.
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