Visualization of distinct DNA regions of the modern human relatively to a neanderthal genome

Diogo Pratas*, Morteza Hosseini, Raquel M. Silva, Armando J. Pinho, Paulo J. S. G. Ferreira

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

3 Citations (Scopus)

Abstract

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.
Original languageEnglish
Title of host publicationPattern Recognition and Image Analysis - 8th Iberian Conference, IbPRIA 2017, Proceedings
EditorsJose Salvador Sanchez, Luis A. Alexandre, Joao M.F. Rodrigues
PublisherSpringer Verlag
Pages235-242
Number of pages8
ISBN (Print)9783319588377, 9783319588384
DOIs
Publication statusPublished - 2017
Externally publishedYes
Event8th Iberian Conference on Pattern Recognition and Image Analysis, IbPRIA 2017 - Faro, Portugal
Duration: 20 Jun 201723 Jun 2017

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume10255 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference8th Iberian Conference on Pattern Recognition and Image Analysis, IbPRIA 2017
Country/TerritoryPortugal
CityFaro
Period20/06/1723/06/17

Keywords

  • Ancient DNA
  • Bloom filters
  • DNA patterns
  • Paleogenomics

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