<abstract xmlns="http://www.w3.org/1999/xhtml"><p>The problem of reads mapping to a reference genome is one of the most essential problems in modern computational biology. The most popular algorithms used to solve this problem are based on the Burrows-Wheeler transform and the FM-index. However, this causes some issues with highly mutated sequences due to a limited number of mutations allowed. G-MAPSEQ is a novel, hybrid algorithm combining two interesting methods: alignment-free sequence comparison and an ultra fast sequence alignment. The former is a fast heuristic algorithm which uses <italic>k</italic>-mer characteristics of nucleotide sequences to find potential mapping places. The latter is a very fast GPU implementation of sequence alignment used to verify the correctness of these mapping positions. The source code of G-MAPSEQ along with other bioinformatic software is available at: <ext-link ext-link-type="uri" xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="http://gpualign.cs.put.poznan.pl">http://gpualign.cs.put.poznan.pl</ext-link>.</p></abstract>

The problem of reads mapping to a reference genome is one of the most essential problems in modern computational biology. The most popular algorithms used to solve this problem are based on the Burrows-Wheeler transform and the FM-index. However, this causes some issues with highly mutated sequences due to a limited number of mutations allowed. G-MAPSEQ is a novel, hybrid algorithm combining two interesting methods: alignment-free sequence comparison and an ultra fast sequence alignment. The former is a fast heuristic algorithm which uses k-mer characteristics of nucleotide sequences to find potential mapping places. The latter is a very fast GPU implementation of sequence alignment used to verify the correctness of these mapping positions. The source code of G-MAPSEQ along with other bioinformatic software is available at: http://gpualign.cs.put.poznan.pl.

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

Institute of Computing Science, Poznan University of Technology, Poland

Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poland

European Center for Bioinformatics and Genomics, Poland

Poznan Supercomputing and Networking Center, Poland

Foundations of Computing and Decision Sciences

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

{"article-title":"G-MAPSEQ \u2013 a new method for mapping reads to a reference genome"}

The problem of reads mapping to a reference genome is one of the most essential problems in modern computational biology. The most popular algorithms used to...

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

Pubblicato online: 02 ago 2016

Pagine: 123 - 142

Ricevuto: 11 gen 2016

Accettato: 12 mag 2016

DOI: https://doi.org/10.1515/fcds-2016-0007

Parole chiave
computational biology, next generation sequencing, parallel computing, reads mapping

© 2016 Pawel Wojciechowski et al., published by De Gruyter Open

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

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

Pubblicato online: 02 ago 2016

Pagine: 123 - 142

Ricevuto: 11 gen 2016

Accettato: 12 mag 2016

DOI: https://doi.org/10.1515/fcds-2016-0007

Parole chiavecomputational biology, next generation sequencing, parallel computing, reads mapping

© 2016 Pawel Wojciechowski et al., published by De Gruyter Open

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.

Parole chiave
computational biology, next generation sequencing, parallel computing, reads mapping