Changes to the GEP Web Framework - Spring 2010

Change log for the Genomics Education Partnership Web Framework
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Changes to the GEP Web Framework - Spring 2010

Post by wleung » Fri Jan 22, 2010 12:55 pm

Hello Everyone,

The GEP web framework has been updated for the Spring semester. The
changes included updates to annotation and finishing packages, updates to
annotation exercises and reset of the project management system. Some of
the annotation web tools have also been updated. Below is a more
comprehensive log of all the changes since Fall 2009:

A. Annotation project updates
1. Annotation packages for D. erecta dot, D. erecta 3L control, and D.
mojavensis dot contains updated BLASTX result against the proteins in D.
melanogaster (release 5.23)

2. Fourteen new annotation packages and genome browser available for the
D. grimshawi dot

As a reminder, in order to synchronize the GEP annotation efforts, all the
GEP resources that reference the D. melanogaster gene models have been
updated to the most recent FlyBase release (release 5.23). Until Ensembl
update their D. melanogaster database records, we recommend that you and
your students use the exon-by-exon listing on the Gene Record Finder or on
FlyBase instead of Ensembl.

B. Finishing project updates
1. Finishing projects from the D. grimshawi dot that still require
sequence improvement are now available for claiming. These projects
have been updated to incorporate traces that were called last year. The
projects also included an additional set of restriction digests that
were done last year.

2. New finishing projects from the D. mojavensis euchromatic control
region is now available to be claimed. These projects have the prefix
DMAC-. The prefix for the fosmid end traces is the name of the project
(e.g. DMAC-1a).

3. Because of problems with the restriction digests last year, the
finishing project packages contain results from the clone as well as its
duplicate partner. Hence for the D. grimshawi projects, there are four
sets of digests: fragSizes.txt, fragSizesb.txt, fragSizesc.txt, and
fragSizesd.txt. The new D. mojavensis projects contain two sets of
digests: fragSizes.txt and fragSizesb.txt.

C. Annotation exercises updates
Many annotation exercises were updated due to substantial changes to the
NCBI web interface. The new exercise packages are compressed using the
zip format. Unlike tar gzip archives (the format we previously used),
all the major platforms can open the zip archives without installing
additional software.

1. A Simple Introduction to NCBI BLAST

2. Exercise #1: Detecting and Interpreting Genetic Homology

3. BLAST Exercise #2: Using mRNA and EST Evidence in Annotation

4. Worksheet: Chimp BAC Analysis: Genes and Pseudogene

5. List of Common Bioinformatics Programs

D. Web tools updates
The following web tools (and their corresponding documentations) have
been updated since Fall 2009:

1. GEP UCSC Genome Browser Mirror
- Updated blastx alignment track to FlyBase release 5.23
- The initial blastx hits are filtered by coverage of the total hit
length and sequence identity

- Once you click on a blastx hit in the new evidence track, you should
see a summary table and a list of alignments that correspond to the
blast hit.

- At the bottom of the page is a link to the dynamic BLAST output
viewer for the blastx results against the contig. Unlike the BLASTX
evidence track on the genome browser, the viewer contains the
unfiltered BLASTX results.

1. Gene Record Finder
- Updated to FlyBase release 5.23
- Redesign interface to highlight CDS's that are shared by multiple

2. Dynamic BLAST Output Viewer
- Added ability to navigate to specific coordinates
- Direct links to FlyBase and Gene Record Finder records in hit
summary table
- General performance improvement and bug fixes

3. Digest Viewer
- Added additional digest images for D. grimshawi projects
- Added new digest images for D. mojavensis control projects

4. GEP Live CD
- Updated image contains Consed version 19
- Added documentation for storing finishing data using external USB
drive or virtual hard drive.

5. GEP Data Repository
- The links in the GEP Data Repository has been updated so that they
point to the new project packages.

Please let me know if you have any questions, concerns, or encounter any
problems with the updated project packages, annotation exercises, or web
tools. Thanks.


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