Schedule Fall 2010

Date

Lecture Notes 
(requires Adobe Acrobat Reader to view)

Book B&O

Assignment

Lecture 1

9/23

DNA and protein databases. Print lecture before class.

Optional reading: 454 Solexa SMRT GenBank RefSeq

Ch. 1

 

Lab. 1

9/23

Basic sequence analyses and submission.

Print the Word document before the lab.

Lab1_Files   Sequin_DNA   Sequin_prot   Sequin_annotation

Assembly Example Key

 

Hwk1 Due 9/30 

MBCS Word Tool Reading

Lecture 2

9/28

Database searching and Sequence alignments  

  Entrez MyNCBI Boolean

Ch. 3

 

Lecture 3

9/30

BLAST

Ch.11

 

Lab. 2

9/30

Sequence Alignment and Database Searches

Lab2_Seqs  FASTA_db

 

Hwk2 Due 10/7  

Hwk2_Seqs

Lecture 4

10/5

Multiple sequence alignments ReviewMSA (read!)

(M-Coffee 3Dcoffee Cobalt-NCBI)

Ch. 12

 

Lecture 5

10/7

Phylogenetics

Ch. 14

 

Lab. 3

10/7

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

 

Hwk3 Due 10/14 

Lecture 6

10/12

Sequence assembly and finishing Lecture notes

Ch. 13

 

Lecture 7

10/14

Sequence annotation  Lecture 7 notes

Ch. 5

 

Lab. 4

10/14

Sequence annotation   

Consensus  Consensus_Annotated  Annotation Powerpoint

Guide to Seq. Annotation 

 

Hwk4 Due 10/21 

Lecture 8

10/19

Comparative genomics  Lecture 8 notes

Ch. 15

 

Lecture 9

10/21

Optional Review Session with TA – Please prepare for the Midterm.

 

 

Lab. 5

10/21

Comparative genomics: genome comparisons

 

No Homework

LabReview

Review

10/22

Review 

10am – 11am in Asmundson 242

 

Midterm

10/26

In class questions plus take home exercises

Due on Monday 11/1 at 12:00 pm by email to TA

 

 

Lecture 11

10/28

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

 

 

Lab. 6

10/28

ESTs : sequencing quality scoring, contigging, data mining and NCBI

 

Hwk6 Due 11/4

Lecture 12

11/2

Genetic Markers, Genetic Mapping
Neale Chapter 3 , Chapter 4

Ch. 2

 

Lecture 13

11/4

QTL mapping
Doerge 2002

 

 

Lab. 7

11/4

Genetic linkage maps. MAPMAKER and QTLs

 

Hwk7 Due 11/11

Hwk Files

Lecture 14

11/9

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

Ch 7

 

 

11/11

Veterans’ Day

 

 

Lecture 15

11/16

SNP Annotation

 

Lecture 16

11/18

Nucleotide diversity & linkage disequilibrium

 

Lab. 8

11/18

SNP discovery: MSAs, quality scores, false discovery rate. Phred Phrap Consed Polyphred

Ch. 7

Hwk8 due 11/25

Lecture 17

11/23

 SNP Genotyping
Syvanen 2001

 

 

 

11/25

Thanksgiving

 

 

Lecture 18

11/30

Association mapping

Ch. 7

 

Lecture 19

12/2

Review

 

Lab. 9

12/2

Association Testing

 

No Homework

Final

12/2

Take home final handed out in Lab on Thursday 12/2.

Due on Thursday 12/9 at noon by email to TA

 

Final

Final

12/10

In Class Exam

 

In Class Final


 

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