II. Report Utilities


D. Genomic-based Reports

1. Genomic-based versus transcript-based organisms.

The database contains two types of sequences, genomic- and transcript-based. Genomic-based sequences are limited to plant genomes or to genomes which are annotated by the ChromDB staff for the DOE Joint Genome Institute . Although genomic sequences are available for other genomes, i.e. Homo sapiens and Drosophila melanogaster, these important model organisms are available as transcript-based only at ChromDB. We depend on sequences from the NCBI Reference Sequence (RefSeq) collection . ChromDB users are cautioned that these RefSeq entries have varying levels of curation.

ChromDB does not display whole chromosome sequences for genomic-based organisms. Genomic sequences are limited to a span of nucleotides which is sufficient to contain the predicted transcript splice model and 5’ and 3’ untranslated regions (UTR).

For ChromDB purposes, GBrowse is a gene browser not a genome browser. The GBrowse thumbnail view on each Gene Record Page is a link to bring up a full GBrowse view. Transcript-based organisms have a GBrowse view that is limited to the transcript and protein domains.

2. Genome-based tools

This report generator uses some of the same features used for the Advanced Search utility.

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.

3. Selection of protein classes (Step 2).
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 in the database

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.

4. Select the type of reports or displays.
a. Protein Description:

This selection displays all proteins classified into that group, as ChromDB IDs and a short description of the protein group.

b. Synonyms:

This selection displays formal names and aliases for the organisms and protein groups selected.

c. Locus:

This tool prepares a list of ChromDB IDs and loci for each gene, if available.

d and e. Protein Domain View for Pfam and SMART domains:

These two separate selections display Pfam or SMART domains views for the selected organism(s) and protein group(s).

f. Number of exons.

This genomic-based specific tool will generate the number of exons comprising a transcript splice model.

g. Exon Viewer.

This genomic-based specific tool will generate a graphical view of alternating exons and introns comprising a transcript splice model. When used in conjunction with the “Number of Exons” selection, a number plus the graphic will appear for each gene selected.

h. Splice Model Status.
This genomic-based specific tool shows the extent of biological data for a transcript splice model. There are three classes of support:
 
i. Transcript splice model confirmed by cDNAs
ii. Transcript splice model partially confirmed by cDNAs
iii. No cDNAs available

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