Organism Specific Navigation with the Brown Tool Bar

The brown toolbar is found at the top of every page in ERGO^TM directly beneath the global green toolbar, but only after the user has set a preferred organism. This toolbar contains access to information and tools that are specific to the preferred organism.

As illustrated above, the organism specific brown toolbar contains three drop-down menus: Data, Query, and Curate.

Data

The following items are available under the Data menu:

Overall Statistics:

displays the statistics page for the organism.

Pfam Domains:

displays all the Pfam domains represented in the organism, along with the number of open reading frames (ORFs) associated with each Pfam domain.

Contigs, Graph:

displays a graphical representation of the contigs of the organism. The blue arrows represent protein-encoding regions ( i.e. ORFs) while the red arrows represent RNA-encoding regions. The direction of the arrows indicates the strand of DNA on which the feature resides. An arrow facing toward the left is on the negative strand, while an arrow facing toward the right is on the positive strand.

If there are public gene aliases available, those will appear above the ORFs. Moving the mouse pointer over any ORF will bring up a tool tip displaying the functional annotation and clicking on it will open up the protein page.

There are several useful coloring options at the bottom of the screen that will highlight ORFs that are of interest. For example, it is possible to highlight ORFs that are involved in any (or all) of the ERGO^TM metabolic pathways. Other availible options include highlighting ORFs that are annotated as a hypothetical protein or by their GC content relative to the average GC content of the entire genome. An option that is useful in comparative genomics allows the user to compare the selected organism to any other availible organism in ERGO^TM. Choosing this option will highlight all ORFs in one organism that have a homolog in the other. To use this option, select "Compare vs. Org" in the "Color ORFs By:" drop down menu and enter the 2 or 3 digit code of the organism with which to be compared in the field labeled "Comparison Organism Code:". Then click "Redraw". The comparison cutoff score may also be adjusted to control the stringency. The region of the genome that is displayed may be adjusted using the "Region" and "Interval Length (in bp)" fields.

Metabolic Overview:

displays the list of metabolic categories. Clicking on any one of these links opens up subcategories that can be further explored. The Metabolic Overview of an organism is built upon biochemical pathways. Continued expansion of a metabolic category leads to a pathway page.

Metabolic Tree:

also described as the Functional Overview, this feature displays a hierarchy of functional categories. The Metabolic Tree also represents a convenient framework for the display of data that can be connected to pathways functions or genes. From the Metabolic Tree, a user may

• Explore any functional category
• Search title, pathway and function names
• Display assertion and/or assignment summaries
• Compare pathways and genes in different organisms
• Assert or unassert pathways
• Display essentiality and microarray expression data

Query

The following items are available under the Query menu:

Functional Hierarchy:

opens up the Metobolic Tree / Functional Overview page in a new window.

By Keywords:

allows the user to search the ERGO^TM database using one or more keywords. The first panel allows users to narrow the search by selecting specific data categories such as ORFs, Pathways, Enzymes, etc. A maximum of 4 keywords may be entered along with AND/OR Boolean operators. Additionally, the search may be limited to a specific organism. This restricts the results to the organism(s) selected. The user may also choose to impose maximum output table length restrictions as well.

By Sequence:

Alternatively, a user is able to search the ERGO^TM database by a DNA or protein sequence. This is advantageous in searches in which the amino acid and/or DNA sequence is known but the functional annotation of the ORF(s) may be absent, incorrect, or lacking the appropriate keyword.

By Pattern:

allows the user to upload a patscan search pattern.

By Protein Properties:

allows a search for proteins based on properties such as length, molecular weight, and isoelectric point. The results can also be filtered by a function so that the results are narrowed to those that contain a particular keyword. If more than one search field is entered, an implied AND is imposed, such that all proteins in the search results will fall into all ranges specified by the user.

By User Annotation:

facilitates searches for ORFs that have been annotated by specific users or include annotations from user models such as Pfam, COGs, or GenBank? .

Export Genome Data:

genomes that are less than 100 megabases in length may be exported in either EMBL format (whole genome) or FASTA format (DNA, protein, and contig). Data is exported in a compressed format (.zip).

Curate