Neandertal Genome Analysis Consortium Tracks at UCSC
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  Neandertal Genome Analysis Consortium Tracks at UCSC



Artist's rendering of Neandertal
Artist's rendering of Neandertal man, from
Neandertal museum in Mettmann, Germany
Copyright: Johannes Krause, Max Planck Institute
for Evolutionary Anthropology
. All rights reserved.

 

Neandertals are the closest extinct relatives of humans. They lived from several hundred thousand years ago until their disappearance approximately 30,000 years ago. The Neandertal genome sequence (published by Green et al. in Science May 2010) consists of short sequence fragments, usually about 50 base pairs long, mapped to the human reference genome. The DNA was extracted largely from three Neandertal bones, each about 40,000 years old, from the Vindija Cave in Croatia: Vi33.16, Vi33.25, and Vi33.26. The bulk sequencing was carried out on the Illumina GAII platform. Neandertal DNA was identified from among the background of microbial sequences in the bone by similarity to the human or chimpanzee genomes.

This portal provides access to the sequence data and alignments to the reference human genome (NCBI Build 36/hg18, GRCh37/hg19) as well as the reference chimpanzee genome (CGSC 2.1/panTro2) and several associated analyses (see Downloads and References).

The following annotations are available on the human hg18 and hg19 genome assemblies, except as noted:

Vindija Cave, Croatia
Entrance of the Vindija Cave, Croatia
Copyright: Johannes Krause, Max Planck Institute for Evolutionary Anthropology. All rights reserved.
Bones from Vindija Cave
The researchers obtained the majority of the DNA used for their study from the bone fragments of three female Neandertals that were excavated in the Vindija Cave in Croatia.
Copyright: Max Planck Institute for Evolutionary Anthropology. All rights reserved.




  Downloads



Data files for tracks at UCSC can be downloaded at the locations below. Files that end with .sql and .txt.gz are dumped from our MySQL database; .sql files name the data fields of each row, and .txt.gz files contain all rows with tab-separated fields. All database dump files have a first column "bin" that can be ignored (it is for database query speedup). Files that end in .bam and .bai contain compressed sequence alignments and index files in the BAM format. The free software packages samtools and PICARD are useful for viewing and manipulating BAM files. The .bw suffix denotes the bigWig format, which stores a numeric signal for genomic positions.

All links below can be fetched using rsync; replace "ftp://" with "rsync://" in the links below.




  Credits



The Neandertal Genome Project was carried out at the Max Planck Institute for Evolutionary Anthropology under the direction of Svante Pääbo and made possible by a grant from the Presidential Innovation Fund of the Max Planck Society.




  References



Neandertal Genome Analysis Consortium (2010):

Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH et al. A draft sequence of the Neandertal genome. Science. 2010 7 May;328(5979):710-22.

Burbano HA, Hodges E, Green RE, Briggs AW, Krause J, Meyer M, Good JM, Maricic T, Johnson PLF, Xuan Z et al. Targeted investigation of the Neandertal genome by array-based sequence capture. Science. 2010 7 May;328(5979):723-5.

Previously published mitochondrial genome of Vi33.16 (2008):

Green RE, Malaspinas AS, Krause J, Briggs AW, Johnson PL, Uhler C, Meyer M, Good JM, Maricic T, Stenzel U, et al. A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell. 2008 Aug 8;134(3):416-26.




  Conditions of Use



The sequence and annotation data displayed in the Genome Browser are freely available for academic, nonprofit, and personal use (see Conditions of Use).