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  About the EmbryoGENE Genome Browser

Bos taurus
Courtesy of Rémi Labrecque

Welcome to the EmbryoGENE Genome Browser, an instance of the UCSC Genome Browser software run at Université Laval.

While developing its transcriptomics and epigenomics platforms, EmbryoGENE has accumulated large amounts of data related to the embryonic Bos taurus genome. This Genome Browser aims to make this data available for public use by the scientific community.

EmbryoGENE's transcriptomics and epigenetics platforms are based on the UMD3.1 assembly of the bovine genome, produced by the Center for Bioinformatics and Computational Biology at University of Maryland. The UMD3.1 assembly is, to date, the most complete and comprehensive assembly of the bovine genome. Until November 1st, 2011, the UCSC Genome Browser did not provide an annotation for this assembly. The EmbryoGENE genome browser was developed to correct this omission.

However on November 1st, the UCSC Genome Browser released bosTau6, an annotation of UMD3.1 which was more feature complete than EmbryoGENE's. Therefore, we have switched from our own database to mirroring UCSC's bosTau6 while providing our own additional custom tracks as a supplement. Such tracks include:

  • The annotation of transcribed features generated by NCBI's Gnomonm as available from CBCB's FTP site.
  • The location of potential new transcripts identified through EmbryoGENE's sequencing experiments.
  • Target sites of the microarray probes from various platforms, including EmbryoGENE's.
  • SNP data.
  • Alternative CpG islands locations, generated through a different methodology from UCSC's CpG Islands track.

To explore this data, the UCSC Genome Browser software offers the following tools:

  • The Genome Browser allows the visualization of genomic regions while displaying annotations of interest.
  • BLAT allows BLAST-like searches of sequences longer than 20 nucleotides on the bovine genome.
  • The In Silico PCR tool predicts the products of a PCR reaction on either genomic or transcribed material.
  • The Table Browser allows cross-referencing the various annotations available on the Genome Browser.


  News

14 May 2013 - Platform presentations

Video presentations for both the transcriptomic platform and the epigenetic platform are now available. AVI files for the presentations can be found in the in the literature and links section.


1 November 2011 - UCSC releases bosTau6

Today, the main UCSC Genome Browser site released its bosTau6 database, an annotation of the UMD3.1 assembly of the Bos taurus genome. Given that the UCSC's annotation is more feature complete than our own, we will be replacing our UMD3.1/bosTau5 database with this new bosTau6 annotation. The original annotation tracks that the EmbryoGENE network has developped that are not redundant with UCSC's will be available in the new database in the EmbryoGENE group.


26 October 2011 - Now Online!

Today marks the public release of the EmbryoGENE Genome Browser. If you have questions or comments, you can send them to Eric Fournier at eric.fournier@fsaa.ulaval.ca.


13 October 2011 - Maintenance

In preparation for the upcoming public release of the EmbryoGENE Genome Browser, the browser will be experiencing intermittent downtime on October 13th and 14th. Be advised that some custom tracks may be lost during the transition.


  Conditions of Use

Use of this genome browser is granted freely for all uses, except for restrictions imposed by the conditions of use of the UCSC Genome Browser. Usage rights of the data from the genome assembly or the associated tracks are dependent on their origin: consult the detail page of a track to determine its source, and consult that source to determine usage conditions.