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Changes to the GEP Web Framework - Fall 2010

Posted: Thu Aug 26, 2010 10:46 pm
by wleung
Hello Everyone,

The Project Management System has been reset for the fall semester. In addition to projects from the D. mojavensis dot, new annotation packages from the D. erecta 3L extended region and the D. grimshawi dot are now available for claiming on the Project Management System. The primary focus for the GEP annotation effort this fall is the D. grimshawi and D. mojavensis dot chromosomes. However, projects from the D. erecta 3L extended region are substantially easier to annotate than the D. grimshawi and D. mojavensis projects. I have updated the ranking on the Project Management System so that the difficulty levels for the D. grimshawi and D. mojavensis projects are higher than the D. erecta projects. As a reminder, the difficulty levels are estimated using the number of significant blastx hits to D. melanogaster proteins, the number of Genscan gene predictions and the overall repeat density. Hence the difficulty level ranking may not genuinely reflect the actual difficulty of a particular project.

I have also reset the Project Management System sandbox so that projects from D. erecta (dot, 3L control, 3L extended), D. mojavensis dot, and the D. grimshawi dot are available for practice. Alternatively, you can download all the project packages through the GEP Data Repository at (under Projects -> GEP Data Repository). You will also find the GAME-XML files for Apollo in the GEP Data Repository.

The annotation report form has also been updated with additional description of the evidence required to file a report when the project sequence does not contain any genes. It also describes the evidence required to support the claim that that a gene prediction is a false positive. All the annotation packages have been updated with the new report form. You can also download a copy of the new report form from the GEP web site at ... report.doc (Curriculum -> Course Materials -> Annotation -> GEP Annotation Report).

Below is the list of key changes to the GEP web framework:

1. Synchronized GEP Web Framework resources to FlyBase Release 5.29
- BLASTX report in the annotation packages, databases for the Gene Record Finder and Gene Model Checker, and the blastx protein alignment track on the Genome Browser have all been updated to release 5.29.

2. UCSC Genome Browser Mirror update
- Upgraded genome browser software to release 238. This release added a few navigation features: including the ability to drag-and-zoom and re-order tracks. I have also enabled the search functionality for the blastx evidence track.

- Added RNA-Seq and TopHat splice site prediction tracks to the D. mojavensis dot chromosome (Sep. 2008) assembly.

- Added D. grimshawi dot (Sep. 2010) assembly

3. Gene Model Checker
- Store gene models form values in browser cookies. This means that all the form values (except for the sequence file) will persist when you refresh the web page.

- Improved detection of overlapping coordinates

- Added a new level (Warn) to the checklist item status:
The following conditions will trigger a warning in the checklist:
a. Non-canonical splice donor site (GC)
b. Number of coding exons differ between the submitted model and the D. melanogaster ortholog

Please provide an explanation for any criteria that has the status “Fail” or “Warn” in the annotation report form.

- Added global alignment between the protein sequence of the submitted model and the D. melanogaster ortholog (under the Dot Plot tab).

- Improved support for Internet Explorer

The documentation for the Gene Model Checker has been updated with descriptions of these new features ... _guide.pdf (Help -> Documentations -> Gene Model Checker User Guide).

4. Gene Record Finder
- Remove “Unique” entry from mRNA Details table.

- Set of unique exons available through the “Export All Unique CDS Sequences” button under “Options”

- Added links to FlyBase protein records and GBrowse

The documentation for the Gene Record Finder has been updated with descriptions of these new features ... _guide.pdf
(Help -> Documentations -> Gene Record Finder User Guide).

Please let me know if you have any questions or encounter any problems with the updated project packages, software programs, or the new genome browser. Thanks.