8

Announcements: read first half of ch. 8 new problem set

Sanger's Method

Neat link to an animated demo

Sanger's process

ddDNA truncates the replication process

Gel electrophoresis spells out the sequence.

And so it comes down to reading a trace

Which sometimes isn't easy

Really not easy

Reads connected by overlapping strings

Needs high coverage to connect everything

Sometimes repeats confound this

Repeat structure

>500 bp sequencing

• Hierarchal
  1. do 150k sequences by shotgun
  2. map them to genome by another process
• Whole Genome Shotgun

Human Genome Project

Use mate-pair information to give global structure

DNA Chips

In the early 90s a process was developed to manufacture DNA chips

Semiconductor lithography techniques useful here

DNA Chips

Probes on the chip hybridize to the whole DNA, in solution

Reconstructing a sequence from its spectrum

Probability of non-uniqueness