Genboree Updates:
« Support Site » There's now a
Genboree Community Support Site. Registered users can access general Genboree
forums and can make feature/fix requests. If you'd like
a forum, issue tracker, wiki, etc, for your Genboree Project
to facilitate collaboration, just ask. We've already done this for some groups!
« Sequence! »
Download hard-masked DNA sequence, if available for your genome.
« Tiling! »
A plug-in for tiling across long annotations in a PCR template track was added.
« Primers! »
By request: more primer-design parameters available! Including specifying
'dead regions' around templates.
« Colors! »
A grid of pre-selected colors now available; or select via the wheel
or in English, decimal RGB, or hex RGB.
« Name-Based Selection! »
Subset annotations from 1+ tracks by names & patterns. Supports both user-defined & existing
gene-specific aliases. Useful for making specific tracks of relevant
genes from larger tracks.
« Sequence! » Can now concatenate all
sequences of an annotation group together. (Eg. all exon sequences of a gene.)
« Colors! »
Each annotation can now have its own color. Useful for emphasis, curating,
or visual subsets. Set colors during upload or manually.
Content News
Genboree News:
« NIH Epigenomics Roadmap Initiative hosted by Genboree »
The Epigenomics Data Analysis and Coordination Center
(EDACC),
a key component of the NIH Epigenomics Roadmap Initiative, will be hosted by Genboree.
« The Cancer Genome Atlas » The Cancer Genome Atlas (TCGA) project has
adopted Genboree for target selection, PCR assay design, quarterly reporting, and mutation capture.
For more information, please refer to this PowerPoint® file.
« Sea Urchin » The Sea Urchin genome has been published, and
its sequence and annotations are now available! You can read more and access the database at The
HGSC Sea Urchin site
. That
database is linked to Genboree, so you can view the annotations in context (
example).
« Rhesus » The Rhesus Macaque genome (rheMac2) is now available as a genomic template within Genboree.
A public database contains assembly- and gene-related tracks,
as well as
BAC-mappings
by end sequences and PGI, and fosmid end mappings.
« H.s. Chr3 » The Human Chr 3 Nature publication is
now available.
Annotations developed and used during the curation effort have been published in Genboree, and many
of the
figures and tables are linked to
the Genboree database.
« H.s. Chr12 » A project page for the
Human Chr12 Nature publication
has been created. The public Genboree database contains annotations from the curation effort.
« Cows » We mapped contigs from the preliminary
cow genome
assembly onto human using
Pash.
The
cow contig mappings
are available through Genboree.
BRL News:
« Genome Portrait of MCF-7 in NYT, Genome Res. »
A map of breakpoints in the MCF-7 breast cancer cell line made by
BRL grad student Oliver A. Hampton is featured in The New York Times
("The Chaos Inside a Cancer Cell")
and is published in Genome Research (Hampton et al., 2008).
« Pash » A new version of Pash, 2.0, has been released! It improves mapping accuracy in the presence of indels,
increases speed by up to a factor of 3 over the previous version, and provides the option of refining Pash anchorings by performing banded alignment.
Contributed by Pash's main developer, Cristian Coarfa. Please see the license and download page to acquire the new version.
« Genomic Triangulation » Our paper
Human-Specific Changes of Genome Structure Detected by Genomic Triangulation
as well our contributions to the
Evolutionary and Biomedical Insights from the Rhesus Macaque Genome paper
have been published.
Data used in the ancestral reconstructions, including genome pairwise comparisons, BAC mappings, fosmid mappings, and markers, as well as the reconstructions themselves and
detected breakpoints are available through
Genboree.
« Pash » A new version of Pash has been released!
Improvements in usage, dependencies, accuracy, scratch space, and small-query mapping; also, the introduction of new scoring methods. Contributed by Pash's main developer,
Cristian Coarfa. Please see the license and download page to acquire the new version.
« H.s. Chr3 & Chr12 » The Human Chr 3 & 12 Nature
articles have been published. Figure 2 in both papers were contributed by
Alan Harris. See the
Genboree news items for more information and links.
« Gap Map » We applied the Gap Map concept to the Rhesus-Human Comparative Linkage Map.
« Rhesus » Our integrated comparative map of rhesus, chimp, and human
includes
matepair chains,
contigs,
and
our latest mappings
of
16,495 Rhesus BACs to the Human genome using the
PGI method.
Note: The rhesus PGI paper
has been published in Genome Research!
« Sequencing » We have developed the Tagamizer program to parse and identify short sequence
tags present in a sequencing read. The Tagamizer program is now
available for download.
![[ View BCM Cow ]](http://www.brl.bcm.tmc.edu/graphics/cow/baylorCow.jpg){kind=link}
