The HuRef  browser was developed at the J. Craig Venter
Institute in support of the Diploid Genome Project
with support from the J. Craig Venter Foundation, under the overall leadership of Sam Levy.
software and tools
The browser uses the following software tools:
external data sources
The HuRef Browser: a web resource for individual human genomics. Axelrod N, Lin Y, Ng PC, Stockwell TB, et al.
The diploid genome sequence of an individual human. Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, et al. PLoS Biol. 2007 Sep 4;5(10):e254.
Tandem repeats finder: a program to analyze DNA sequences. Benson, G. Nucleic Acids Research (1999) Vol. 27, No. 2, pp. 573-580.
Istrail, S., Sutton, C.G., Florea, L., Halpern, A.L., Mobarry, C.M. et al. (2004) Whole-genome shotgun assembly and comparison of human genome assemblies. Proc. Natl. Acad. Sci. USA 101: 1916-1921.
Karolchik, D., Baertsch, R., Diekhans, M., Furey, T.S., Hinrichs, A., Lu, Y.T., Roskin, K.M., Schwartz, M., Sugnet, C.W., Thomas, D.J., Weber, R.J., Haussler, D. and Kent, W.J. The UCSC Genome Browser Database. Nucl. Acids Res 31(1), 51-54 (2003).
Furey, T.S., and Haussler, D. Integration of the cytogenetic map with the draft human genome sequence, Hum. Mol. Gen., 12(9), 1037-1044 (2003).
Heinicke S., Livstone M.S., Lu C., Oughtred R., Kang F., Angiuoli S.V., White O., Botstein D., Dolinski K.(2007) The Princeton Protein Orthology Database (P-POD): A Comparative Genomics Analysis Tool for Biologists.PLoS ONE 2:e766.
Version 1.0, December 19th, 2008
- Added a menu when the user clicks on any feature that enables the user to:
- Center the current view on the feature
- Export the feature in FASTA format
- Open the Feature in the Inspector window
- Highlight the Feature in the Sequence Alignment
- NCBI's dbSNP database: release 124
- Added a menu when the user clicks on the ruler that enables the user to:
- Center the current view on the location
- Identify features that overlap any single base location
- Added functionality to enable the user to track their cursor location using the horizontal ruler.
- The haplotype phasing is displayed in the multiple sequence alignment component. The alleles are highlighted using the same color to denote the association of reads to their respective haplotypes for any heterozygous variant column in the alignment.
- Added a button to flip the strand in View
- Display functionally significant SNPs at high-level (histogram) View
Version 0.9, May 30th, 2008
Imported and enabled searching by:
- NCBI human gene models annotated on HuRef (syntax: geneid[number])
- RefSeq accessions (syntax: n|x|m_[number])
- NCBI accessions of HuRef contigs and scaffolds (syntax: CTG_[number])
- New Assembly View with histogram plots of clone coverage
- Added contig track to assembly view
- Improved display of compound tracks and histogram plots
- Ability to easily "flip" the reference axis between NCBI and HuRef
- New export as FASTA option for any feature (URL syntax: export.cgi?search=[query])
- Improved ability for users to manage and maintain configuration of the display
- Improved display of inversions
Version 0.8.2, February 11th, 2008
- Fixed a series of bugs that were caused by a non-globally unique DOM node id namespace.
- Added 15 sec timeouts to all XML HTTP Requests, and appropriate timeout callback function.
- Fixed issue in IE 6.0 with dynamically adding checkboxes to use special IE checkboxNode.defaultChecked attribute.
Version 0.8.2, February 11th, 2008
- Fixed a bug caused by invalid search queries. If any search fails to return a valid feature, the browser application loads a default region and displays an appropriate error message.
- Searches for dbSNP or HuRef variants now shows the multiple sequence alignment highlighting the region where the variant sequence is found.
- Added Back/Forward Internet browser navigation functionality using the dojo.undo.browser Api.
Version 0.8.1, January 28, 2008
- The initial public release of the HuRef Diploid Human Genome Browser.
There are many individuals that contributed to the design and development of the HuRef browser. For the sake of brevity, we wish to thank a few of our contributors here:
- Nelson Axelrod
- Yuan Lin
- Jonathan Crabtree
- Tim Stockwell
- Dr. Jiaqi Huang
- Dr. Pauline Ng
- Dr. Ewen Kirkness
- Dr. Saul Kravitz
- Dr. Samuel Levy
comments and questions