Courtesy of Rémi Labrecque
Welcome to the EmbryoGENE Genome Browser, an instance of the
UCSC Genome Browser software run at
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
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.