21.10.2014 - 17:12
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Contact

Prof. Dr. Svante Pääbo

Director, Department of Genetics

Max Planck Institute for Evolutionary Anthropology

Deutscher Platz 6
04103 Leipzig

phone: +49 341 3550 - 500
fax: +49 341 3550 - 555

e-mail: paabo@[>>> Please remove the brackets! <<<]eva.mpg.de

Data

Whole Genome

The 1x Neandertal genome sequence was generated from 6 Neandertal fossils from different locations:

  • Vindija cave, Croatia: Vi33.16 (54.1% genome coverage), Vi33.25 (46.6%) and Vi33.26 (45.2%).
  • Neander Valley, Germany (the Neandertal type specimen): Feld1 (0.1%)
  • El Sidron cave, Asturias, Spain: Sid1253 (0.1%)
  • Mezmaiskaya, Altai Mountains, Russia: Mez1 (2%)

All sequence reads

All sequence data generated from Neandertal fossils
http://www.ebi.ac.uk/ena/data/view/ERP000119

All sequence data for 5 modern humans
http://www.ebi.ac.uk/ena/data/view/ERP000121

Alignments

Alignments for all Neandertal sequences to the human and chimpanzee genomes are available from in BAM format. Download here.

Alignments for all Neandertal sequences to the human and chimpanzee genomes Neandertal reads were mapped to the human genome (hg18), using a custom mapper called ANFO (http://bioinf.eva.mpg.de/anfo). This custom alignment program was developed to take the characteristics of ancient DNA into account. Following the observation and implementation by Briggs et al. {Briggs, 2009 Science}, ANFO uses different substitution matrices for DNA thought to be double stranded versus single stranded and changes between them if doing so affords a better score.

For each library, consensus sequences were constructed from multiple reads of the same Neandertal molecule, defined as having the same orientation, read length, alignment length, and alignment start coordinates. All such clusters, regardless of their mapping quality, are replaced by their consensus sequence. For each observed base and each possible original base, we calculated the likelihood of the observation from its quality score. The base with the highest quality score (calculated by dividing each likelihood by the total likelihood) is used as the consensus.

Genome Browsers

Explore the Neandertal genome using the Ensembl or UCSC Genome Browser frameworks. These browsers provide tools for genome comparison and analysis:
The Neandertal Genome at Ensembl: http://projects.ensembl.org/neandertal/
The UCSC Neandertal Genome Browser: http://genome.ucsc.edu/Neandertal/