I. Search Functions
Genes, proteins, organisms and information in ChromDB can be accessed in the following ways:
B. Advanced Search for Information Retrieval:
The Advance Search feature is a useful way to search for and retrieve information regarding ChromDB genes. This feature can be accessed from the left side style sheet or from the link next to the Quick Search Text Box. There are three different options, or entry points, associated with the Advanced Search 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 choices will be explained below; click on a subject to jump forward).
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 will be explained below; click on a subject to jump to any of the links).
Note: The speed of the data retrieval is decreased with increased numbers of selections.
Please be patient.2. Step 2: Selection of protein classifications.
Over 90 different protein groups exist in the database. The options listed below provide access to a functional-type of classification or proteins group and an alphabetical listing of the groups.
a. Option 1: Selection using functional groupings
The menu selection in Step 2 presents a higher order grouping of the ChromDB 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
"Select a protein group" in Step 2 is a link that brings up a new page with an alphabetical listing of all protein groups in the database. Each protein group includes a three to five letter abbreviation followed by a short description of that 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 typing in the name.
Note: Multiple protein groups can be made with either option, but increasing numbers of groups will slow the retrieval process. Please be patient.
3. Step 3: Select the type of reports or displays
This selection displays all proteins classified into the selected group(s). The output includes the ChromDB IDs and a short description of each protein.
This selection displays formal names and aliases for the organisms and protein groups selected.
The last two selections are for viewing either or both Pfam or SMART domains for the selected organisms and protein groups. An additional link for the protein domain viewer is included on the side tool bar.
Note: The speed of viewing a final report decreases with increasing the number of selections; please be patient.
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