Selecting Regions Overview Panel Detail Panel Adding Annotations Quick Uploads

Generic Genome Browser: General Help

These are general instructions for using the Generic Genome Browser. This page should be customized by the administrator of this resource to describe site-specific features.

Selecting a Region of the Genome

To select a region of the genome to view, enter its name in the text field labeled "Landmark or Region". Recognized types of names are under the control of the administrator, but usually the following names are accepted:

a chromosome name
For genomes that have been assembled into chromosome-length segments, you can enter the name of the chromosome. The chromosome name follows the conventional nomenclature for the species. For example, C. elegans chromosomes are indicated using roman numerals, such as III, D. melanogaster uses chromosome arms such as 2L and 2R, while H. sapiens uses arabic numbers such as 9.

a gene name
You can enter the name of a gene using the standard nomenclature for that species.

a contig or clone name
You can enter the name of a structural landmark such as a cosmid, BAC or contig.

an accession number
You can enter a GenBank or EMBL accession number.

protein names, primer names, ORF IDs, author names...
At the discretion of the administrator of the database, other identifiers can be entered. See the examples listed at the top of the browser page for hints.

The Overview and Detail Panels

If the landmark is found in the database, the browser will display the region of the genome it occupies. The region is displayed in two graphical panels:

overview panel
This panel displays the genomic context, typically an entire assembled chromosome or a large portion of the sequence assembly such as a scaffold or contig. At the administrators' discretion, certain important landmarks, such as a well-known genetic markers or cytogenetic bands can be placed in this view. A red rectangle indicates the region of the genome that is displayed in the detail panel. This rectangle may appear as a single line if the detailed region is relatively small.

detail panel
This panel displays a zoomed-in view of the genome corresponding to the overview's red rectangle. The detail panel consists of one or more tracks showing annotations and other features that have been placed on the genome. The detail panel is described at length later.

If the requested landmark is not found, the browser will display a message to this effect.

Specifying the Landmark Class

At the administrator's option, some kinds of landmarks may have to be qualified with their "class" using the format class:landmark. For example, to look up the PCR product sjj_K08A8.1 in the C. elegans database, you will search for PCR_Product:sjj_K08A8.1.

In the case of clashes between names, such as a contig and a gene both named c23, you can use the name class to specify which landmark you mean.