Schedule Fall 2009

Date

Lecture Notes 
(requires Adobe Acrobat Reader to view)

Book B&O

Assignment

Lecture 1

9/24

DNA and protein databases. Print lecture before class.

Optional reading: 454 Solexa SMRT GenBank RefSeq

Ch. 1

 

Lab. 1

9/24

Basic sequence analyses and submission. Print the Word document before the lab.

Files for Lab1

 

Hwk1 due 10/1 by email

Files for Hwk1

Hwk1 KEY

Lecture 2

9/29

Database searching and Sequence alignments    Entrez MyNCBI Boolean

Ch. 3

 

Lecture 3

10/1

BLAST

Ch.11

 

Lab. 2

10/1

Sequence Alignment and Database Searches

 

Hwk2 due 10/8 by email

Hwk2 KEY

Lecture 4

10/6

Multiple sequence alignments ReviewMSA M-Coffee 3Dcoffee

Ch. 12

 

Lecture 5

10/8

Phylogenetics

Ch. 14

 

Lab. 3

10/8

Multiple Sequence Alignment and Phylogenetics: UPGMA, Neighbor Joining, and Parsimony algorithms. MEGA4. 

 

Hwk3 due 10/15 by email

Hwk3 KEY

Lecture 6

10/13

Sequence assembly and finishing Lecture notes

Ch. 13

 

Lecture 7

10/15

Sequence annotation Lecture 7 notes

Ch. 5

 

Lab. 4

10/15

Sequence assembling and sequence annotation 

Guide to Seq. Annotation

 

Hwk4 due 10/22 by email

Files for Hwk4

Hwk4 KEY

Lecture 8

10/20

Comparative genomics Lecture 8 notes

Ch. 15

 

Lecture 9

10/22

Review

 

 

Lab. 5

10/22

Comparative genomics: genome comparisons

 

No Homework

LabReview

PptReview

Midterm

10/27

In class questions plus take home exercises

Due on Monday 11/2 at 10:00 am by email to TA

 

Take-home exercises

Take-home files

Take-home Exam KEY

Lecture 11

10/29

Expressed Sequence Tags (ESTs)
Chapter 12 Baxevanis & Ouellette (2nd edition)

 

 

Lab. 6

10/29

ESTs : sequencing quality scoring, contigging, data mining and NCBI (pdf)

 

Hwk6 due 11/5 by email

Hwk6_trace_files.zip

Hwk6 KEY

Lecture 12

11/3

Genetic Markers
Neale Chapter 4

Ch. 2

 

Lecture 13

11/5

Genetic Mapping
Neale Chapter 3 

 

 

Lab. 7

11/5

Genetic linkage maps. MAPMAKER (pdf)

 

Hwk7 due 11/12 by email

Hwk7 KEY

Lecture 14

11/10

Complex traits

Neale Chapter 18  

 

 

 

11/11

Veterans’ Day

 

 

Lectures 15

11/12

QTL mapping
Doerge 2002

Ch. 7

 

Lab. 8

11/12

QTL mapping: software and algorithms

PDF Version

 

Hwk8 due 11/19 by email

(Note- right click and save the files)

File1  File2

Hwk8 KEY

Lecture 16

11/17

SNP Discovery
Marth et al. 1999   Nickerson et al. 1997
Picoult-Newberg et al. 1999

Ch. 7

 

Lecture 17

11/19

 Nucleotide diversity & linkage disequilibrium

 

 

Lab. 9

11/19

SNP discovery: MSAs, quality scores, false wdiscovery rate.

Phred Phrap Consed

 

Hwk9 due 12/1 by email

Hwk9 KEY

Lecture 18

11/24

Selection and tests of neutrality

Ch. 7

 

 

11/26

Thanksgiving

 

 

Lecture 19

12/1

SNP Genotyping
Syvanen 2001

Ch. 7

 

Lecture 20

12/3

Association mapping

Ch. 2

 

Lab. 10

12/3

Nucleotide Diversity Analysis
Rozas 2003 DnaSP

BeadStudio and TASSEL Demos

 

No Homework

Final

12/3

Take home final handed out in Lab on Thursday 12/3.

Due on Thursday 12/10 at noon by email to TA

 

Final

Final KEY

Final

12/8

In Class Exam 10:30AM-12:30PM  Please be on time.

ROOM: Young 192

 

In Class Final

 

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