Processing may take a few seconds...

Article

Download file

Title

G-MAPSEQ – a new method for mapping reads to a reference genome

Authors

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

Year of publication

2016

Published in

Foundations of Computing and Decision Sciences

Journal year: 2016 | Journal volume: vol. 41 | Journal number: no. 2

Article type

scientific article

Publication language

english

Keywords
EN
  • computational biology
  • next generation sequencing
  • parallel computing
  • reads mapping
Abstract

EN The problem of reads mapping to a reference genome is one of themost essential problems in modern computational biology. The most popular algo-rithms used to solve this problem are based on the Burrows-Wheeler transform andthe FM-index. However, this causes some issues with highly mutated sequences dueto a limited number of mutations allowed. G-MAPSEQ is a novel, hybrid algorithmcombining two interesting methods: alignment-free sequence comparison and an ultrafast sequence alignment. The former is a fast heuristic algorithm which usesk-mercharacteristics of nucleotide sequences to find potential mapping places. The latteris a very fast GPU implementation of sequence alignment used to verify the correct-ness of these mapping positions. The source code of G-MAPSEQ along with otherbioinformatic software is available at: http://gpualign.cs.put.poznan.pl.

Pages (from - to)

123 - 142

DOI

10.1515/fcds-2016-0007

URL

https://www.sciendo.com/article/10.1515/fcds-2016-0007

License type

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

Open Access Mode

open journal

Open Access Text Version

final published version

Date of Open Access to the publication

at the time of publication

Full text of article

Download file

Access level to full text

public

Points of MNiSW / journal

15.0

This website uses cookies to remember the authenticated session of the user. For more information, read about Cookies and Privacy Policy.