Sequencing A Large Genome

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Announcements

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Methods for Sequencing a Genome

Clone-by-Clone: Physical Mapping

Whole Genome Shotgun Sequencing

Reconstructing the Sequence (Fragment Assembly)

Unfortunately…

Advantages & Disadvantages of Each Method

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ARACHNE: Steps to Assemble a Genome

1. Find Overlapping Reads

1. Find Overlapping Reads (cont’d)

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2. Merge Reads into Contigs (cont’d)

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4. Derive Consensus Sequence

Simulated Whole Genome Shotgun

Making a Simulated Read

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Neurospora crassa Genome (Real Data)

Computational Resources

ARACHNE in the Near Future

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Whole Genome Sequencing by Walking with Clone-ends: A Mathematical Analysis

The Walking Method

Description of Walking Method

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Walking off a Single Seed

Walking off Several Seeds in Parallel

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Closing an Ocean: Picture

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Revisiting our Assumptions

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Collaborators

Lecturer: Manolis Kamvysselis

Author: Serafim Batzoglou

Email: serafim@cs.stanford.edu

Home Page: http://theory.lcs.mit.edu/~bab/01-18.417-home.html

Other information:
18.417 Fall 2001
Serafim Batzoglou
For class use only