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Title

DNA sequence assembly involving an acyclic graph model

Authors

[ 1 ] Instytut Informatyki, Wydział Informatyki, Politechnika Poznańska | [ P ] employee | [ D ] phd student

Year of publication

2013

Published in

Foundations of Computing and Decision Sciences

Journal year: 2013 | Journal volume: Vol. 38 | Journal number: no. 1

Article type

scientific article

Publication language

english

Keywords
EN
  • DNA sequence assembly
  • acyclic graph model
  • GPU programming
Abstract

EN The problem of DNA sequence assembly is well known for its high complexity. Experimental errors of di erent kinds present in data and huge sizes of the problem instances make this problem very hard to solve. In order to deal with such data, advanced efficient heuristics must be constructed. Here, we propose a new approach to the sequence assembly problem, modeled as the problem of searching for paths in an acyclic digraph. Since the graph representing an assembly instance is not acyclic in general, it is heuristically transformed into the acyclic form. This approach reduces the time of computations significantly and allows to maintain high quality of produced solutions.

Pages (from - to)

25 - 34

DOI

10.2478/v10209-011-0019-4

URL

https://sciendo.com/article/10.2478/v10209-011-0019-4

License type

CC BY-NC-ND (attribution - noncommercial - no derivatives)

Full text of article

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Access level to full text

public

Points of MNiSW / journal

15.0

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