MGI Mouse Genome Browser on build GRCm38
MGI Mouse Genome Browser on build GRCm38
A number of tracks have been removed from this GBrowse instance. These tracks have been moved to our new JBrowse sequence browser. Please use that instead. The tracks that remain are updated weekly with the JBrowse load.
We are replacing our MGI GBrowse instance with GMOD's newer sequence browser... JBrowse. It incorporates a faster, more flexible platform for users as well as an active development community. In the future please visit the new browser. GBrowse will still be used in the near future but a large majority of the tracks here will be being removed.
We have started adding curated locations for miRNA clusters. These are incorporated in the MGI Genome Features track labeled as "miRNA Cluster." As an example see Mirc7.
We have now incorporated a number of remote tracks from the UCSC Genome Browser via Bio DAS. These tracks include...
For more information on each of these tracks please look at their site.
Our genome browser now includes QTL's and VISTA Enhancers!
QTL locations are being given genome coordinates according to submitted peak or flanking markers as published by the authors in the original papers. The curation effort is ongoing and we will be adding new QTL's with each update. To enable this track go to the "Select Tracks" Tab and check the box next to "MGI QTLs". Because some of these regions are very large this track can be viewed all the way out to chromosome level.
With ENSEMBL Release 71 one of many additions was the mapping of VISTA enhancers to build 38. We have incorporated these into a track and it can be found under the sequence subsection of the Select Tracks tab. For more information on VISTA enhancers visit their website.
We have added in a new STS track containing all placed DNA segments from MGI. This track can be found under the sequence category in the select track tab along with all of the BAC end tracks. Because the data in this track is more sparse the track can be viewed at a 10MB window before changing to a density view.
We have changed our MGI Genome Features track to be more informative by including MGI Feature Type to all entries. We have also added a number of pseudogenes and genes that no longer have a model in current genome builds. These orphaned gene models are colored in yellow. Another change in conjunction with this is in our Gene Traps "per gene" track we are only displaying those genes with gene traps rather than all genes. We have also enabled the browser to show large scale density representations on tracks. Zooming out past 1MB enables this view on all of the tracks except the GRC genome issues track. Finally we have a basic mouse/human synteny browser up and running here. It is currently displaying Synteny data from Mouse Mine that compares mouse genes from our MGI Genome Feature track to Human Genes from NCBI. Stay tuned for more development on this new feature.
We have added a new track containing information from three DbVar datasets. This includes Keane et al. 2011(estd118), Wong et al. 2012(estd200), and Yalcin et al. 2012(estd185). This track is color coded showing either gain(blue), loss(red) or other(black). The strain that each individual variation was found in is printed in blue below each entry. This track can be found in the select tracks tab under the General Category. For more information on this track please see their corresponding page in NCBI's DbVAR.
We have added in four new BAC end libraries to the browser. These include...
These can be accessed under the Select Tracks Tab in the Clone Libraries catagory. For more information on these libraries please see their corresponding page in NCBI's CloneDB
The MGI Mouse Genome browser has now been updated to build 38. We have also upgraded our browsing software so that we are now running GBrowse Version 2.39 that we will continue to develop with new functionalities.
So far we have recreated a number of tracks from the build 37 instance of the browser...
We have also added a few new tracks that were not in the previous release. These include...
We will be activly maintaining these tracks as they are updated and we plan to add a number of new tracks in the near future.
If you have any additional tracks you would like to see on MGI's Mouse Genome Browser please let us know.
Paul Hale Jan 2013