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Human Reference Genome Browser

Posted by pbio on 07 May 2009 at 22:24 GMT

Author: Samuel Levy
Position: Director, Human Genomics
Institution: J. Craig Venter Institute
E-mail: slevy@jcvi.org
Additional Authors: Nelson Axelrod, Yuan Lin, Jonathan Crabtree, Timothy Stockwell, Saul Kravitz.
Submitted Date: April 30, 2008
Published Date: May 1, 2008
This comment was originally posted as a “Reader Response” on the publication date indicated above. All Reader Responses are now available as comments.

The Human Reference (HuRef) Genome Browser is a Web application for the navigation and analysis of the single human diploid genome of J. Craig Venter as recently published in PLoS Biology. It is now available online at http://huref.jcvi.org.

The HuRef database consists of approximately 32 million DNA reads sequenced using Sanger methods, assembled into 4,528 scaffolds and 4.1 million DNA variations identified by genome analysis. These variants include Single Nucleotide Polymorphisms (SNPs), block substitutions, short and large indels, structural variants like insertion, deletions, inversions and copy number changes.

The browser enables scientists to navigate the HuRef genome assembly and sequence variations, and to compare it with the NCBI human build 36 assembly in the context of the NCBI and Ensembl annotations. The browser provides a comparative view between NCBI and HuRef consensus sequences, the sequence multi-alignment of the HuRef assembly, Ensembl and dbSNP annotations, HuRef variants, and the underlying variant evidence and functional analysis. The interface also represents the haplotype blocks from which diploid genome sequence can be inferred and the relation of variants to gene annotations. The display of variants and gene annotations are linked to external public resources including dbSNP (www.ncbi.nlm.nih.gov/SNP), Ensembl (www.ensembl.org), Online Mendelian Inheritance in Man (OMIM: www.ncbi.nlm.nih.gov/omim) and Gene Ontology (GO).

Users can search the HuRef genome using HUGO gene names, Ensembl and dbSNP identifiers, HuRef contig or scaffold locations, or NCBI chromosome locations. Users can then easily and quickly browse any genomic region via the simple and intuitive pan and zoom controls; furthermore relevant data in specific loci can be exported for further analysis.

No competing interests declared.