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Changes to the GEP Web Framework - Fall 2011

Posted: Sat Aug 20, 2011 6:14 pm
by wleung
Hello Everyone,

The Project Management System has been reset for the fall semester. Projects from the D. mojavensis 3L region and the D. erecta 3L extended region are available for claiming though the Project Management System.

The primary focus for the GEP annotation efforts this year is the set of projects derived from the D. mojavensis 3L region. However, because projects from D. erecta are substantially easier to annotate than D. mojavensis, I have also created a new set of 50 D. erecta projects (listed under the 3L 2nd extended assembly on the Genome Browser Gateway page) in the event that additional D. erecta projects are needed. These D. erecta projects are currently posted on the GEP UCSC Genome Browser and the GEP Data Repository but will not be available for claiming until all the projects from the current 3L extended region have been claimed.

As a reminder, the estimated difficulty of an annotation project is based on the number of significant blastx hits to D. melanogaster proteins, the number of Genscan gene predictions, and the overall repeat density. Consequently, the project difficulty ranking may not necessarily reflect the actual difficulty of a given project.

The biggest change this year is the incorporation of mRNA-Seq data into the Genome Browser. Same-species mRNA-Seq evidence tracks are available for D. mojavensis, D. ananassae, and D. virilis. Cross-species mRNA-Seq evidence tracks are available for D. erecta and D. grimshawi. All the mRNA-Seq data tracks are listed under the “RNA Seq Tracks” section on the Genome Browser.

Dr. Buhler has developed a new exercise that illustrates how the new RNA-Seq data can be used in annotation. The exercise is titled “Browser-Based Annotation and RNA-Seq Data” and it is available at ... naseq_hwk2.

An overview of the RNA-Seq evidence tracks from my Alumni Workshop presentation is available at ... e0811.pptx.

We have also made many improvements to the GEP web framework. The key changes are listed below:

1. Synchronized GEP Web Framework resources to FlyBase Release 5.39
- 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 5.39.

2. UCSC Genome Browser Mirror update
- Added modENCODE RNA-Seq evidence tracks
- Added newly finished projects from D. mojavensis 3L reference region
- Created new genome browser for the D. erecta 3L 2nd extended region (Sep. 2011 release)

3. Gene Model Checker
- Color Dot plot and global alignments, where the alternating colors represent individual exons
- Added new warning to detect unknown ortholog names

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

4. Gene Record Finder
- New naming convention for unique exons identifiers
- Export CDS and exon usage table as Excel Workbooks

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

5. Annotation Files Merger
- Added link to view merged GFF file in the Genome Browser
- Added the Isoform Checklist when merging GFF files to verify the ortholog names and number of isoforms in the merged GFF file

The documentation for annotation project submission has been updated with descriptions of these new features. Please see ... ations.pdf
(Help -> Documentations -> Web Framework ->Submit Annotation Projects) for details.

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