TY - GEN
T1 - Visualization of distinct DNA regions of the modern human relatively to a neanderthal genome
AU - Pratas, Diogo
AU - Hosseini, Morteza
AU - Silva, Raquel M.
AU - Pinho, Armando J.
AU - Ferreira, Paulo J. S. G.
N1 - Funding Information:
We thank Martin Kircher, for very helpful comments and explanations, and Cláudio Teixeira, for computational infrastructures. This work was funded by FEDER (Programa Operacional Factores de Competitividade - COMPETE) and by National Funds through the FCT - Foundation for Science and Technology, in the context of the projects UID/CEC/00127/2013 , UID/BIM/04501/2013 , PTCD/EEI-SII/6608/2014 and the grant SFRH/BPD/111148/2015 to RMS.
Publisher Copyright:
© Springer International Publishing AG 2017.
PY - 2017
Y1 - 2017
N2 - Species-specific DNA regions are segments that are unique or share high dissimilarity relatively to close species. Their discovery is important, because they allow the localization of evolutionary traits that are often related to novel functionalities and, sometimes, diseases. We have detected distinct DNA regions specific in the modern human, when compared to a Neanderthal high-quality genome sequence obtained from a bone of a Siberian woman. The bone is around 50,000 years old and the DNA raw data totalizes more than 418 GB. Since the data size required for localizing efficiently such events is very high, it is not practical to store the model on a table or hash table. Thus, we propose a probabilistic method to map and visualize those regions. The time complexity of the method is linear. The computational tool is available at http://pratas.github.io/chester. The results, computed in approximately two days using a single CPU core, show several regions with documented neanderthal absent regions, namely genes associated with the brain (neurotransmiters and synapses), hearing, blood, fertility and the immune system. However, it also shows several undocumented regions, that may express new functions linked with the evolution of the modern human.
AB - Species-specific DNA regions are segments that are unique or share high dissimilarity relatively to close species. Their discovery is important, because they allow the localization of evolutionary traits that are often related to novel functionalities and, sometimes, diseases. We have detected distinct DNA regions specific in the modern human, when compared to a Neanderthal high-quality genome sequence obtained from a bone of a Siberian woman. The bone is around 50,000 years old and the DNA raw data totalizes more than 418 GB. Since the data size required for localizing efficiently such events is very high, it is not practical to store the model on a table or hash table. Thus, we propose a probabilistic method to map and visualize those regions. The time complexity of the method is linear. The computational tool is available at http://pratas.github.io/chester. The results, computed in approximately two days using a single CPU core, show several regions with documented neanderthal absent regions, namely genes associated with the brain (neurotransmiters and synapses), hearing, blood, fertility and the immune system. However, it also shows several undocumented regions, that may express new functions linked with the evolution of the modern human.
KW - Ancient DNA
KW - Bloom filters
KW - DNA patterns
KW - Paleogenomics
UR - http://www.scopus.com/inward/record.url?scp=85021224756&partnerID=8YFLogxK
U2 - 10.1007/978-3-319-58838-4_26
DO - 10.1007/978-3-319-58838-4_26
M3 - Conference contribution
AN - SCOPUS:85021224756
SN - 9783319588377
SN - 9783319588384
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 235
EP - 242
BT - Pattern Recognition and Image Analysis - 8th Iberian Conference, IbPRIA 2017, Proceedings
A2 - Salvador Sanchez, Jose
A2 - Alexandre, Luis A.
A2 - Rodrigues, João M. F.
PB - Springer Verlag
T2 - 8th Iberian Conference on Pattern Recognition and Image Analysis, IbPRIA 2017
Y2 - 20 June 2017 through 23 June 2017
ER -