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


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

Year of publication


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


  • computational biology
  • next generation sequencing
  • parallel computing
  • reads mapping

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:

Pages (from - to)

123 - 142




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

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