I. Search Functions

Genes, proteins, organisms and information in ChromDB can be accessed in the following ways:

A. Quick Search text box options:

1. Gene name or synonym (alias):

Use the Quick Search text box as a rapid way to access a particular gene of interest or to determine if a gene is included in the database. This search function allows you to type in an official gene symbol, a synonym (alias), or the ChromDB Identifier (ID) for a particular gene or protein. The same ChromDB ID is used for both the gene and protein; gene and protein are used interchangeably in this document.
Example:
 
The ChromDB ID for the Arabidopsis thaliana DDM1 gene or protein is CHR1; either name will display the DDM1/CHR1 gene record page.
Note: If you enter an official gene symbol that is used for multiple organisms, you will be presented with a list of ChromDB IDs, each of which has that name as the official name or an alias.

Example: AGO1 typed into the Quick Search text box will return:
ChromDB ID = AGO1 for the Arabidopsis AGO1 gene/protein
ChromDB ID = AGO401 for the Drosophila AGO1 gene/protein
ChromDB ID = AGO601 for the Schizosaccharomyces AGO1 gene/protein

2. Locus:

Arabidopsis thaliana, Oryza sativa ssp. japonica (japonica rice), Drosophila melanogaster, Saccharomyces cerevisiae, and Schizosaccharomyces pombe genes can be accessed by entering the proper locus designation in the "Quick Search" text box. The text box will accept only one locus at a time. Viewing of multiple loci can be accomplished using the Loci link listed under the "Reports" section found in the style sheet section on the left side of ChromDB web pages.

3. Organism:

Database users can type in an organism, either the formal or common name, and retrieve an output containing three columns, i.e. the formal name and the common name of the organism, as well as a list that shows the number of proteins in the database which are associated with that organism. The formal name is a link to the appropriate taxonomy page at NCBI, and the number is a link for displaying a list of genes in the database.

This search function is flexible in that a query will bring up an exact match to a whole name, as well as any organism name that includes the string of letters used as a query. This search function is a way to retrieve the formal name of the organism, which is necessary for some of the information retrieval tools.

Note: When using the protein number link to form a list of proteins, please be patient as the retrieval process time depends on the number of proteins to be displayed.

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