Neandertal Genome Browser
The Neandertal Genome Project has sequenced six samples from members of Homo sapiens neanderthalensis. Almost 98% of the sequence comes from three specimens from the Vindija Cave in Croatia; most of the remainder comes from an individual from Mezmaiskaya in the Altai Mountains, Russia, with tiny fractions (0.1%) from the species type specimen (Neander valley, Germany) and a fossil found in El Sidron cave in Asturias, Spain. To put the Neandertal sequences in perspective, the project also sequenced five modern humans, Homo sapiens sapiens, from Southern Africa, Western Africa, Papua New Guinea, China and Europe.
The Neandertal sequences were mapped to the human reference genome (NCBI36), the chimpanzee genome, and an ancestral sequence extrapolated from a 4-way EPO alignment between human, chimp, orangutan and macaque, using a custom alignment program that takes into account the characteristics of ancient DNA.
Comparison of the aligned data has been used to locate SNPs, producing tracks that can be displayed in the Neandertal Genome Browser alongside the human reference genome using the Distributed Annotation System (DAS).
The Neandertal Genome Project is based at the department of Evolutionary Genetics at the Max Planck Institute for Evolutionary Anthropology in collaboration with the Neandertal Genome Consortium. The Neandertal Genome Browser uses code developed by Ensembl, a joint project of the EBI and the Wellcome Trust Sanger Institute.