Topical
Outline
Spring 2008 Schedule
Reading List
This course is a joint offering of the Departments of Pathobiology and Medical Education and Biomedical Informatics, and the Institute for Public Health Genetics. It forms part of the curriculum for the Ph.D. program in Pathobiology, and the M.S. program in Genetic Epidemiology within the Institute of Public Health Genetics, and is open to students and postgraduate trainees in the biomedical, computer, and information sciences who are interested in molecular sequence databases and sequence analysis. The course provides an introduction to the accumulation, analysis, and retrieval of biological sequence information in the context of computer-based informatics, the Internet, and world-wide databases. Topics covered include the biological, biochemical, and evolutionary criteria for understanding the relevance of biological sequence information, techniques for the accumulation of protein and DNA sequences, computer-based manipulation and analysis of sequence information, descriptions of available biological and biochemical databases, and the methods for database accession and interrogation. Various computer software, search algorithms, and Internet resources are discussed. The course consists of bi-weekly lectures and computer lab sessions.
Prerequisite:
Permission of instructor. Faculty and staff are invited to audit.
Contact Tim Rose (616-2084, trose@u.washington.edu) for further information.
Abbreviated title:
Bioinfo & Seq Anal
Instructors:
Dr. Timothy Rose, Professor, Pediatrics
Dr. Peter Myler, Research Professor, Pathobiology
Evaluation:
Class evaluation will be based on weekly assignments and a take-home final.
1: Introduction to
biological sequence information - Nucleotides and DNA; Gene and
chromosomal structure; DNA regulatory elements; Amino acids and polypeptides;
Protein functional domains; Gene families and superfamilies.
2: Internet based resources, including
the National Center for Biotechnology Information (NCBI) - Internet Sequence databases,
centers, and servers; The NCBI Entrez/Pubmed system; Navigational aids to Web
resources; Software databases and archives
3: DNA analysis - Nucleotide
composition; Restriction site analysis; Primer selection and design; Sequence
comparisons - dot plots and alignments; Translation and open reading frame
analysis.
4: Protein analysis
- Amino acid composition and mol. wt. prediction; Identification of
protein motifs; Protein secondary structure prediction; Protein modification.
5: Database similarity searching -
Sequence homology; Search algorithms and programs; Local and global alignments;
Scoring matrices; BLAST database searching; Interpreting search results.
6: Pattern and motif analysis -
DNA regulatory elements; Protein domains and motifs; Pattern databases;
Searching for conserved domains and motifs.
7: EST analysis – Expressed
sequence tag analysis and EST databases; mRNA structure.
8: SNP analysis – Single nucleotide
polymorphism analysis and SNP databases; nucleotide mutations.
9: Genome sequencing and genome analysis – Large
scale sequencing techniques and whole genome analysis; genome databases.
10: Gene prediction – gene structure;
prediction programs
11: Multiple sequence alignments - Sequence alignment basics; sequence conservation.
12: Phylogenetic analysis - Methods of
estimating evolutionary distance; Phylogenetic tree prediction and
interpretation
13:
Protein structure analysis - Protein structure databases;
Modeling of protein structure; protein structure similarity searches.
Email -- bioinfo@u.washington.edu
Web -- http://courses.washington.edu/bioinfo/
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