Bioinformatics Tools, Databases, and Methods
UCSC Extension

Bioinformatics Courses I teach

Next Offering

Check the UCSC extension catalog. When the course is offered next, and enrollment is open, click here .

Lecture Topics and Schedule

This is the list of topics that I cover in this course, approximately one per week. Other instructors may or may not cover exactly the same topics in the same schedule, however I expect their lists to be similar.

  1. Sequence Databases: GenBank, EMBL, file formats.
  2. Text-based Database Searches: Entrez, SRS, DBGET.
  3. Sequence-Based Database Searches: BLAST, FASTA.
  4. Motif Databases and Motif-based Searches: PROSITE, Pfam.
  5. Pairwise and Multiple Alignment: Local and global alignment, BLAST2Sequences, progressive alignment. CLUSTALW.
  6. Phylogenetic Analysis: distance-based methods, parsimony, maximum-likelihood, PHYLIP.
  7. GCG: The Wisconsin Package.
  8. Sequence analysis tools: prediction of physico-chemical properties; prediction of sites, gene finding.
  9. Structure Databases and Search Tools: PDB, file format. VAST, DALI.
  10. Other Databases: Specialized sequence databases. Microarray databases. Map databases.

Course Description (as in catalog)

With the explosion of biomolecular sequence and structure data now widely available, the field of bioinformatics is playing a crucial role in its storage, search, and analysis. A significant amount of data is now available over the world wide web, along with software tools for its search and analysis. Knowledge of these databases and tools is essential for those working with biological sequences or structures in both the public and private sector.

This practical course provides an introduction to the main public domain tools, databases and methods in bioinformatics including DNA and protein databases such as Genbank and PDB, software tools including BLAST, and methods including those for aligning sequences. It emphasizes the needs of the user of the bioinformatics tools and databases, rather than an emphasis on complex algorithm development and advanced computational methods. However, students that are computer scientists will be provided the opportunity to gain an understanding of the fundamental methods in bioinformatics (e.g. alignment algorithms) in sufficient detail to implement them through optional programming assignments.

The lectures will include some on-line demonstrations of databases and tools on the world wide web.

Prerequisites (as in UCSC extension catalog)

Introduction to Molecular Biology. Access to the internet and the world wide web, and web browsing experience is required outside of class. Data Analysis, Modeling and Visualization for Bioinformatics is desired, but not required. No programming experience is needed.

Texts

The required text is Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Edited by A.D. Baxevanis and B.F. Francis Ouellette, .

The following material is nice Trends Guide To Bioinformatics, Trends Supplement 1998, Elsevier Trends Journals but a bit difficult to find. Try Amazon.com or Elsevier.