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Bioinformatics
BIO/MIC 440/540
The term bioinformatics is often used as a synonym for
"biocomputing" or "computational biology".
This field uses computers to study living systems and applies computer
science and information technology to biological problems.
Much of the data analyzed in bioinformatics is molecular in nature, i.e.
the sequence of nucleotides in DNA or RNA, or the amino acids in a protein.
Being able to manipulate and study this information is the basis for the current
revolution in Biotechnology. Students
with a strong background in bioinformatics will have many job opportunities in
both corporate and academic settings. This course also gives students an
opportunity to see the relationships between biology, microbiology, chemistry
and computer science.
J-term Syllabus
Spring Syllabus
Grading
J-Term Grades
Sites we will use often in class
Syllabus J-Term 2008
Format:
2 Credits.
4-1/2 hours per day, Jan 7-18.
150 Murphy
Instructors:
Unit 1
Marc Rott (Microbiology)
rott.marc@uwlax.edu
785-6965
Unit 2
Bonnie Bratina (Microbiology)
bratina.boni@uwlax.edu
785-6994
Unit 3
Anne Galbraith (Biology)
galbrait.anne@uwlax.edu
785-8246
Unit 4
Scott Cooper
(Biology)
cooper.scot@uwlax.edu
785-6983
UNIT
1 Introduction to Databases and Alignments
| Mon., Jan
7
|
Lecture: Background in Molecular Biology/
Introduction to bioinformatics.
Lab: Sequence databases (Genbank & Swissprot,
dbEST, 16S rRNA, etc).
Reference databases (PubMed, OMIM). Entrez.
Lecture: Theory behind database searches and sequence
alignments. Biology Workbench.
Lab: Homology searches (BLAST, FASTA, etc.) |
| Tue., Jan 8
|
Lecture: Theory behind database searches
and sequence alignments (cont.).
Lab: Sequence Alignments (BLAST 2
Sequences).
|
UNIT 2 RNA
| Wed., Jan 9 |
Quiz 1
Quiz1
Lecture:
Identification of organisms using SSU rRNA. Aligning multiple
sequences.
Lab: Taxonomic databases (NCBI, 16S rRNA database). Multiple
alignments (CLUSTALW).
|
| Thurs., Jan 10 |
Take-home assignment 1 due.
Lecture:
Creating phylogenetic trees from
SSU rRNA protein and DNA sequences.
Lab: Generation of phylogenetic trees. Design of
species-specific probes. |
UNIT 3 Genomes
| Fri., Jan. 11 |
Quiz2
Lecture:
Genome mapping, types of maps, use of molecular markers.
Lab: Contig assembly, using molecular markers, HapMap.
Lecture: Using genomic DNA sequences to discover genes.
Lab: ORF prediction and work with GENSCAN.
|
| Mon., Jan. 14 |
Take-home assignment 2 due.
"J-Term Break"
Lecture: Comparative genomics, study of entire
genomes.
Lab: Comparative genomics, alignments. |
| Tue., Jan. 15 |
Lecture: Functional genomics, microarrays.
Lab: Microarray analysis. |
UNIT 4 Protein Structure
| Wed., Jan. 16 |
Quiz3
Lecture:
Prediction of protein structure, protein families.
Lab:
Prediction of protein structure
(secondary structure, membrane spanning, motifs). Alignment of multiple
protein sequences (CLUSTALW). Prediction of protein activity (metabolic
databases).
|
| Thurs., Jan. 17 |
Take-home assignment 3 due.
Lecture:
Molecular modeling.
Lab: Molecular
modeling of protein families. Molecular modeling of the same protein from
several species (Protein Explorer with multiple sequence alignment
coloring). |
| Fri., Jan. 18 |
Lecture: Overview and review.
Lab: Complete take-home assignment.
Quiz4 and Take-home assignment 4 due. |
|
|
Syllabus Spring 2008
Format:
2 Credits.
2:15- 5:20, Tuesday and Thursday, 150 Murphy Library (7-week
course)
Instructors:
Unit 1
Mike Abler (Biology)
abler.mich@uwlax.edu
785-6962
Unit 2
Bonnie Bratina (Microbiology)
bratina.boni@uwlax.edu
785-6994
Unit 3
Mike Abler (Biology)
abler.mich@uwlax.edu
785-6962
Unit 4
Todd Weaver (Chemistry)
weaver.todd@uwlax.edu 785-8269
UNIT 1 Introduction to Databases and Alignments
|
Jan 29
|
Introduction to bioinformatics. Sequence databases (Genbank &, Swissprot, dbEST, 16S rRNA,
etc). Reference databases (PubMed,
OMIM). Entrez.
|
|
Jan 31
|
Database searches (BLAST, FASTA, etc).
Exercise 1 due.
|
|
Feb 5
|
Sequence
Alignments (BLAST 2 Sequences).
|
UNIT 2 RNA
|
Feb 7
|
Quiz1
Identification of organisms using SSU rRNA. Aligning multiple
sequences.
|
|
Feb 12
|
Take-home
assignment 1 due.
Multiple alignments (CLUSTALW).
|
|
Feb 14 |
Creating phylogenetic trees from SSU rRNA protein and DNA sequences.
|
UNIT 3 Genomes
|
Feb 19
|
Quiz2
Genome mapping (STS, RFLP,
radiation hybrid, comparative mapping).
|
|
Feb 21
|
Take-home assignment 2 due.
Using genomic DNA sequences to discover genes.
ORF prediction and gene families.
|
|
Feb 26 |
Comparative genomics |
|
Feb 28 |
EST's, functional
genomics
|
UNIT 4 Protein Structure
|
Mar 4
|
Quiz3
Prediction of protein structure (secondary structure, membrane
spanning, motifs).
|
|
Mar 6
|
Take-home
assignment 3 due.
Alignment of multiple protein sequences (CLUSTALW).
Prediction of protein activity (metabolic databases)
|
|
Mar 11
|
Molecular modeling of protein families.
Protein evolution and phylogenetics
Molecular modeling of the same protein from several species.
(Protein Explorer with multiple sequence alignment coloring)
|
|
Mar 13 |
Quiz4 and Take-home assignment 4 due.
Free time to complete independent
assignment |
Grading:
Quizzes
25 points each (x4)
Take-home assignments
50 points each (x4)
Total
300 points
A 92-100%
AB 88-92%
B 81-88%
BC 77-81%
C 70-77%
D 60-70%
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