About the HuRef Browser

The HuRef [1] 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:

sequence data

The underlying sequence data for the project was generated at Celera Genomics and the J. Craig Venter Institute's Joint Technology Center.

external data sources

  • NCBI's human sequence assembly: release 36.1
  • Ensembl's annotation on this assembly: release 41.36c
    Data from the following independent sources was also obtained from this Ensembl release:
    • NCBI's dbSNP database: release 124
  • The UCSC Genome Browser's chromosome band data: release hg18. [4]
    The chromosome band data used in the HuRef browser was downloaded from the cytoBandIdeo table in the hg18 UCSC Genome Browser Database [5]
  • Entrez Gene's MIM and GO mapping files: downloaded from ftp.ncbi.nlm.nih.gov/gene/
  • P-POD (Princeton Protein Orthology Database): downloaded in September, 2007 [6]

references

  1. 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.
  2. Tandem repeats finder: a program to analyze DNA sequences. Benson, G. Nucleic Acids Research (1999) Vol. 27, No. 2, pp. 573-580.
  3. 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.
  4. 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).
  5. 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).
  6. 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.

release notes

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.

acknowledgements

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

Please contact us with questions or comments via hurefhelp@jcvi.org.