Reference-based DNA shotgun sequencing: Information theoretic limits

Soheil Mohajer, Abolfazl Motahari, David Tse

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Scopus citations

Abstract

The reference-based DNA shotgun assembly problem is studied from an information-theoretic point of view. The entire sequence has to be assembled based on a reference sequence which is a noisy version of the desired one, and a set of short reads sampled from the desired sequence. Two necessary conditions on the underlying parameters for reconstruction are obtained. A reference-based assembly algorithm is proposed, and it is shown that under these conditions the algorithm can reconstruct the sequence with high probability.

Original languageEnglish (US)
Title of host publication2013 IEEE International Symposium on Information Theory, ISIT 2013
Pages1635-1639
Number of pages5
DOIs
StatePublished - Dec 19 2013
Event2013 IEEE International Symposium on Information Theory, ISIT 2013 - Istanbul, Turkey
Duration: Jul 7 2013Jul 12 2013

Publication series

NameIEEE International Symposium on Information Theory - Proceedings
ISSN (Print)2157-8095

Other

Other2013 IEEE International Symposium on Information Theory, ISIT 2013
CountryTurkey
CityIstanbul
Period7/7/137/12/13

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