Algorithms for mapping high-throughput DNA sequences
Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
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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
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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