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it - Information Technology

Methods and Applications of Informatics and Information Technology

Editor-in-Chief: Molitor, Paul

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2196-7032
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Volume 58, Issue 3 (Jun 2016)

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A history of DNA sequence assembly

Eugene W. Myers Jr
Published Online: 2016-06-25 | DOI: https://doi.org/10.1515/itit-2015-0047

Abstract

DNA sequence assembly is a rich combinatorial problem that arose with the first DNA sequencing projects in the early 80's. Here we give a short history of the progression of algorithmic ideas used to solve the de novo problem of inferring a genome given a large sampling of substrings covering it. This classic inverse problem is compounded by a variety of experimental features and artifacts that must be considered in any realistic solution. While current methods produce very good results, the perfect assembler has yet to be built.

Keywords: Shotgun sequencing; shortest common superstring; string graph; de Bruijn graph

ACM CCS: Applied computing →Life and medical sciences →Computational biology →Sequencing and genotyping technologies

About the article

Eugene W. Myers Jr

Prof. Dr. Gene Myers Jr became the founding director of the Center for Systems Biology Dresden within the Max-Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) in 2012. Previously Gene had been a group leader at the HHMI Janelia Farm Research Campus (JFRC) since its inception in 2005. Gene came to the JFRC from UC Berkeley where he was on the faculty of Computer Science from 2003 to 2005. He was formerly Vice President of Informatics Research at Celera Genomics for four years where he and his team determined the sequences of the Drosophila, Human, and Mouse genomes using the whole genome paired-end shotgun technique that he advocated in 1997. Prior to that Gene was on the faculty of the University of Arizona for 17 years and he received his Ph.D in Computer Science from the University of Colorado in 1981.

Max Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany


Accepted: 2016-03-09

Received: 2015-10-26

Published Online: 2016-06-25

Published in Print: 2016-06-28


Citation Information: it - Information Technology, ISSN (Online) 2196-7032, ISSN (Print) 1611-2776, DOI: https://doi.org/10.1515/itit-2015-0047.

Export Citation

©2016 Eugene W. Myers Jr, published by De Gruyter GmbH Berlin/Boston.. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License. BY-NC-ND 3.0

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