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UID:www.tcs.tifr.res.in/event/717
DTSTAMP:20230914T125935Z
SUMMARY:Information Theory of DNA Shotgun Sequencing
DESCRIPTION:Speaker: Varun Narayanan\n\nAbstract: \nDNA sequencing is the b
 asic workhorse of modern day biology and medicine. Shotgun sequencing is t
 he dominant technique used: many randomly located short fragments called r
 eads are extracted from the DNA sequence\, and these reads are assembled t
 o reconstruct the original sequence. A basic question is: given a sequenci
 ng technology and the statistics of the DNA sequence\, what is the minimum
  number of reads required for reliable reconstruction? This number provide
 s a fundamental limit to the performance of any assembly algorithm. In thi
 s seminar\, we will discuss a paper with the above title by David Tse from
  2013. For a simple statistical model of the DNA sequence and the read pro
 cess\, We find that the answer admits a critical phenomenon in the asympto
 tic limit of long DNA sequences: if the read length is below a threshold\,
  reconstruction is impossible no matter how many reads are observed\, and 
 if the read length is above the threshold\, having enough reads to cover t
 he DNA sequence is sufficient to reconstruct. The threshold is computed 
 in terms of the Renyi entropy rate of the DNA sequence.\n
URL:https://www.tcs.tifr.res.in/web/events/717
DTSTART;TZID=Asia/Kolkata:20161014T160000
DTEND;TZID=Asia/Kolkata:20161014T173000
LOCATION:A-201 (STCS Seminar Room)
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