New Course:

Application of Bioinformatics in Genetics Research (GMS 6014)

This course is designed to help graduate students understand the basics of bioinformatic applications and enable them to apply these tools in a more efficient and creative manner.

Topics covered in the course include:

Sequence and bio-information representation,

Sequence analysis,

Sequence comparison and similarity search,

Protein structure prediction,

Advanced database searching,

Genomic data analysis,

Phylogenetic analysis,

Gene ontology and systems biology.

In addition to lectures, students will have hands-on experience (using the computer facility provided by Health Science Center Library) in the following areas:

·  Sequence analysis and similarity search.

·  Advanced Entrez and expression database query.

·  Analyzing DNA array data using popular applications.

·  Write simple programs to crunch your own sequence.

·  Etc.

Lecturers:

Dr. Henry Baker

Dr. Michele Tennant

Dr. Lei Zhou (course director)

Textbook:

Bioinformatics: Sequence and Genome Analysis. By David W. Mount. Cold Spring Harbor Laboratory Press 2001.

Enrollment limit: 15 (due to the availability of computers in the classroom)

Syllabus: (tentative, subject to change) Module 3, Spring 2003

Date / Topics / Contents / Instructor
1 / Introduction / ·  Introduction,
·  IUPAC-IUB codes for AA and NA,
·  Sequence Format – FASTA, GeneBank, SwissProt / LZ
2 / Bio-Databases I. / ·  Types of DB (archival vs. curated)
·  DB query skills
·  Entrez – Field, limit, RefSeq, and Locus -link / MT
3 / Public software development platforms for bioinformatics. / ·  Intro to Open-source platforms – Java, Perl, Python
·  Download and compile program / LZ
4 / Sequence alignment. / ·  Uses of sequence alignment
·  Dot matrix alignment
·  Global vs. local alignment
·  Scoring matrix / LZ
5 / Homology search –I. / ·  Scoring matrix and measurement of similarity
·  BLAST, FASTA and Smith-Waterman algorithm / LZ
6 / Homology search –II. / ·  Statistical parameters in BLAST analysis
·  Phi-Blast and Psi-blast
·  Customization of BLAST analysis / LZ
7 / Sequence patterns (motifs). / ·  Uses of pattern (motif) analysis
·  Transcription factor binding sites
·  Motif databases- BLOCK, PROSITE, Pfam / LZ
8 / HMM-based motif analysis. / ·  Basics of HMM
·  How are HMM trained
·  Other uses of HMM / LZ
9 / Protein structure analysis. / ·  Different algorithms
·  Examples / L.Z.
10 / Phylogenetic analysis. / ·  Taxonomy
·  Phylogenetic analysis
·  Cross genome comparison / M.T.
11 / Genomic data maintenance and analysis I. / ·  Intro to Genomic studies
·  Genome annotation information
·  Management of genomic/proteomic data / H.B.
12 / Genomic data maintenance and analysis II. / ·  Analysis of Genomic/Proteomic data
n  data normalization
n  statistical analysis / H.B.
13 / Functional Genomics. / ·  Transcription network
·  Data specification for functional information / H.B
14 / Bio-Databases II. / ·  Intro to SAGE
·  Gene Expression and Variation DB / M.T.
15 / Systems biology and integration of information. / ·  Systems biology concept
·  Examples of systems biology effort
·  Gene Ontology / LZ