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The UCSC Genome Browser database: update 2011.

Nucleic acids research | Jan 23, 2011

The University of California, Santa Cruz Genome Browser (http://genome.ucsc.edu) offers online access to a database of genomic sequence and annotation data for a wide variety of organisms. The Browser also has many tools for visualizing, comparing and analyzing both publicly available and user-generated genomic data sets, aligning sequences and uploading user data. Among the features released this year are a gene search tool and annotation track drag-reorder functionality as well as support for BAM and BigWig/BigBed file formats. New display enhancements include overlay of multiple wiggle tracks through use of transparent coloring, options for displaying transformed wiggle data, a 'mean+whiskers' windowing function for display of wiggle data at high zoom levels, and more color schemes for microarray data. New data highlights include seven new genome assemblies, a Neandertal genome data portal, phenotype and disease association data, a human RNA editing track, and a zebrafish Conservation track. We also describe updates to existing tracks.

Pubmed ID: 20959295 RIS Download

Mesh terms: Animals | Databases, Genetic | Disease | Genes | Genome, Human | Genomics | Hominidae | Humans | Internet | Molecular Sequence Annotation | Phenotype | RNA Editing | Software

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Associated grants

  • Agency: NCI NIH HHS, Id: U24CA143858
  • Agency: NHGRI NIH HHS, Id: P01HG5062
  • Agency: NICHD NIH HHS, Id: RC2HD064525
  • Agency: NHGRI NIH HHS, Id: U41HG004568
  • Agency: NIEHS NIH HHS, Id: U01ES017154
  • Agency: NHGRI NIH HHS, Id: U01HG004695
  • Agency: NHGRI NIH HHS, Id: U41HG004269
  • Agency: Howard Hughes Medical Institute, Id: P41HG002371
  • Agency: NHGRI NIH HHS, Id: U54HG004555
  • Agency: NHGRI NIH HHS, Id: U01DE20057
  • Agency: NIDCR NIH HHS, Id:

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1000 Genomes: A Deep Catalog of Human Genetic Variation

International collaboration producing an extensive public catalog of human genetic variation, including SNPs and structural variants, and their haplotype contexts, in an effort to provide a foundation for investigating the relationship between genotype and phenotype. The genomes of about 2500 unidentified people from about 25 populations around the world were sequenced using next-generation sequencing technologies. Redundant sequencing on various platforms and by different groups of scientists of the same samples can be compared. The results of the study are freely and publicly accessible to researchers worldwide. The consortium identified the following populations whose DNA will be sequenced: Yoruba in Ibadan, Nigeria; Japanese in Tokyo; Chinese in Beijing; Utah residents with ancestry from northern and western Europe; Luhya in Webuye, Kenya; Maasai in Kinyawa, Kenya; Toscani in Italy; Gujarati Indians in Houston; Chinese in metropolitan Denver; people of Mexican ancestry in Los Angeles; and people of African ancestry in the southwestern United States. The goal Project is to find most genetic variants that have frequencies of at least 1% in the populations studied. Sequencing is still too expensive to deeply sequence the many samples being studied for this project. However, any particular region of the genome generally contains a limited number of haplotypes. Data can be combined across many samples to allow efficient detection of most of the variants in a region. The Project currently plans to sequence each sample to about 4X coverage; at this depth sequencing cannot provide the complete genotype of each sample, but should allow the detection of most variants with frequencies as low as 1%. Combining the data from 2500 samples should allow highly accurate estimation (imputation) of the variants and genotypes for each sample that were not seen directly by the light sequencing. All samples from the 1000 genomes are available as lymphoblastoid cell lines (LCLs) and LCL derived DNA from the Coriell Cell Repository as part of the NHGRI Catalog. The sequence and alignment data generated by the 1000genomes project is made available as quickly as possible via their mirrored ftp sites. ftp://ftp.1000genomes.ebi.ac.uk ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes

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