1. We recreated the
entire database incorporating the genome of Pythium ultimum.
2. We rewrote nearly all of the code for much greater efficiency.
3. We changed the capability to show a series of best BLAST hits
for any gene into the capability to show genes of closest distance,
calculated using a substitution matrix, and based on a global pairwise
4. We based all clustering on distance scores rather than identity
scores and show these values throughout the presentation.
5. We refined the way that genes are chosen to appear in the Synteny
6. We created pages that explain details of the presentation for
each of the Details Pages, Cluster and Compare Pages, and Synteny
7. We eliminated the construction of separate trees that vary in
8. We changed the phylogenetic method to Neighbor Joining.
9 . We corrected an error in the way that CDS length is calculated.
1. We added a bug report
2. We created this page and
added a link to it from the landing page.
3. We fixed the temporarily broken links from
the cluster and compare pages to the synteny pages.
1. We made scores of
cosmetic changes and we changed terminology in many places to clarify
and improve consistency.
2. We added the capability to search on VMD Gene ID to both the
landing page query and the details page query.
3. We built pages that describe our PHRINGE system and added links
from the landing page.
4. We added a table that describes all cluster types to the genome
5. We added the feature of show/hide the cluster details and the
intron-exon structures on the cluster and compare pages.
6. We added links from the landing page to details about each genome
7. We added a link to our details page for each gene that calls
up the corresponding page at the VMD site.
8. We added to this same field the capability of retrieving the
analogous files from the Broad Institute for each gene of P. infestans.
9. We created a version control system for managing updates to the
site and have a test site for verifying any changes before updating
to the next version.
10. We downloaded all of the VMD gene description lines and created
a field in our gene details pages that shows this.
11. We added the VMD gene description
lines to the pop up box on the synteny page.
12. We added the scaffold number and gene position number and both
our PHRINGE gene ID numbers and your VMD gene ID numbers (or Broad
ID numbers for P. infestans) to the pop up box on the synteny page,
then reorganized this information into a more sensible order.