Algorithms for mapping high-throughput DNA sequences

Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

Standard

Algorithms for mapping high-throughput DNA sequences. / Frellsen, Jes; Menzel, Peter; Krogh, Anders.

Comprehensive Biomedical Physics: Bioinformatics. ed. / Anders Brahme. Vol. 6 Elsevier, 2014. p. 41-50 (Reference Module in Biomedical Sciences, Vol. 6).

Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review

Harvard

Frellsen, J, Menzel, P & Krogh, A 2014, Algorithms for mapping high-throughput DNA sequences. in A Brahme (ed.), Comprehensive Biomedical Physics: Bioinformatics. vol. 6, Elsevier, Reference Module in Biomedical Sciences, vol. 6, pp. 41-50. https://doi.org/10.1016/B978-0-444-53632-7.01103-5

APA

Frellsen, J., Menzel, P., & Krogh, A. (2014). Algorithms for mapping high-throughput DNA sequences. In A. Brahme (Ed.), Comprehensive Biomedical Physics: Bioinformatics (Vol. 6, pp. 41-50). Elsevier. Reference Module in Biomedical Sciences Vol. 6 https://doi.org/10.1016/B978-0-444-53632-7.01103-5

Vancouver

Frellsen J, Menzel P, Krogh A. Algorithms for mapping high-throughput DNA sequences. In Brahme A, editor, Comprehensive Biomedical Physics: Bioinformatics. Vol. 6. Elsevier. 2014. p. 41-50. (Reference Module in Biomedical Sciences, Vol. 6). https://doi.org/10.1016/B978-0-444-53632-7.01103-5

Author

Frellsen, Jes ; Menzel, Peter ; Krogh, Anders. / Algorithms for mapping high-throughput DNA sequences. Comprehensive Biomedical Physics: Bioinformatics. editor / Anders Brahme. Vol. 6 Elsevier, 2014. pp. 41-50 (Reference Module in Biomedical Sciences, Vol. 6).

Bibtex

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title = "Algorithms for mapping high-throughput DNA sequences",
abstract = "Abstract High-throughput sequencing (HTS) technologies revolutionized the field of molecular biology by enabling large scale whole genome sequencing as well as a broad range of experiments for studying the cell's inner workings directly on DNA or RNA level. Given the dramatically increased rate of data generation, new bioinformatics approaches have been developed to cope with the large amount of sequencing reads obtained in these experiments. In this chapter, we first introduce HTS technologies and their usage in molecular biology and discuss the problem of mapping sequencing reads to their genomic origin. We then in detail describe two approaches that offer very fast heuristics to solve the mapping problem in a feasible runtime. In particular, we describe the BLAT algorithm, and we give an introduction to the Burrows-Wheeler Transform and the mapping algorithms based on this transformation.",
keywords = "Algorithms, High-throughput sequencing, Mapping",
author = "Jes Frellsen and Peter Menzel and Anders Krogh",
year = "2014",
doi = "10.1016/B978-0-444-53632-7.01103-5",
language = "English",
isbn = "978-0-444-53633-4",
volume = "6",
series = "Reference Module in Biomedical Sciences",
publisher = "Elsevier",
pages = "41--50",
editor = "Anders Brahme",
booktitle = "Comprehensive Biomedical Physics",
address = "Netherlands",

}

RIS

TY - CHAP

T1 - Algorithms for mapping high-throughput DNA sequences

AU - Frellsen, Jes

AU - Menzel, Peter

AU - Krogh, Anders

PY - 2014

Y1 - 2014

N2 - Abstract High-throughput sequencing (HTS) technologies revolutionized the field of molecular biology by enabling large scale whole genome sequencing as well as a broad range of experiments for studying the cell's inner workings directly on DNA or RNA level. Given the dramatically increased rate of data generation, new bioinformatics approaches have been developed to cope with the large amount of sequencing reads obtained in these experiments. In this chapter, we first introduce HTS technologies and their usage in molecular biology and discuss the problem of mapping sequencing reads to their genomic origin. We then in detail describe two approaches that offer very fast heuristics to solve the mapping problem in a feasible runtime. In particular, we describe the BLAT algorithm, and we give an introduction to the Burrows-Wheeler Transform and the mapping algorithms based on this transformation.

AB - Abstract High-throughput sequencing (HTS) technologies revolutionized the field of molecular biology by enabling large scale whole genome sequencing as well as a broad range of experiments for studying the cell's inner workings directly on DNA or RNA level. Given the dramatically increased rate of data generation, new bioinformatics approaches have been developed to cope with the large amount of sequencing reads obtained in these experiments. In this chapter, we first introduce HTS technologies and their usage in molecular biology and discuss the problem of mapping sequencing reads to their genomic origin. We then in detail describe two approaches that offer very fast heuristics to solve the mapping problem in a feasible runtime. In particular, we describe the BLAT algorithm, and we give an introduction to the Burrows-Wheeler Transform and the mapping algorithms based on this transformation.

KW - Algorithms

KW - High-throughput sequencing

KW - Mapping

U2 - 10.1016/B978-0-444-53632-7.01103-5

DO - 10.1016/B978-0-444-53632-7.01103-5

M3 - Book chapter

SN - 978-0-444-53633-4

VL - 6

T3 - Reference Module in Biomedical Sciences

SP - 41

EP - 50

BT - Comprehensive Biomedical Physics

A2 - Brahme, Anders

PB - Elsevier

ER -

ID: 132349938