eprintid: 2684
rev_number: 14
eprint_status: archive
userid: 326
dir: disk0/00/00/26/84
datestamp: 2018-06-08 08:51:51
lastmod: 2018-06-08 08:51:51
status_changed: 2018-06-08 08:51:51
type: conference_item
metadata_visibility: show
creators_name: Nguyen, Thi Phuong Thao
creators_name: Le, Sy Vinh
creators_id: thaontp@ioit.ac.vn
creators_id: vinhls@vnu.edu.vn
title: Building minimum recombination ancestral recombination graphs for whole genomes
ispublished: pub
subjects: IT
divisions: fac_fit
abstract: Building ancestral recombination graphs (ARGs) with the minimum number of recombination events is an essential problem in genomic population studies. Exhaustive search methods have been proposed to solve the problem with few sequences and markers. Recently, we introduced ARG4WG algorithm [1] to build plausible ARGs for whole genomes of thousand samples. However, the ARG4WG algorithm was not designed to optimize the number of recombination events. In this work, we propose a new design of the ARG4WG algorithm to optimize the number of recombination events. The key idea is to analyze and combine different criteria (i.e., the longest shared ends, the maximum similarity between sequences, and the length of sequences) to select the best candidates for recombinations. The experiments on different data sets showed that our new algorithms produced ARGs with smaller number of recombination events in comparison to other methods. The methods allow us to build minimum recombination ARGs from whole genome data sets.
date: 2017-11-24
date_type: published
full_text_status: public
pres_type: paper
pagerange: 248-253
event_title: 2017 4th NAFOSTED Conference on Information and Computer Science (NICS 2017)
event_location: Hanoi, Vietnam
event_dates: 24-25 November 2017
event_type: conference
refereed: TRUE
citation:   Nguyen, Thi Phuong Thao and Le, Sy Vinh  (2017) Building minimum recombination ancestral recombination graphs for whole genomes.  In: 2017 4th NAFOSTED Conference on Information and Computer Science (NICS 2017), 24-25 November 2017, Hanoi, Vietnam.     
document_url: https://eprints.uet.vnu.edu.vn/eprints/id/eprint/2684/1/thao2017.pdf