Pharm 207/Bio 207 

Using Internet Resources in Molecular Biology - Fall 2003
Course Instructors:

Prof. Philip E. Bourne PhD

TA: Kristine Briedis

Location: San Diego Supercomputer Center Room 116  [map]
Graduate Student Course, 2 Credits
Last Update October 14, 2003

Students with laptops and wireless Internet connections are encouraged to bring them to class

Course Outline | External Internet Resources | Assignment


Increasingly the Internet is a source both of data and analysis tools  in the field of molecular biology. Knowing what is available, being able to use these resources, and to interpret results returned by these resources is important to principal investigators, fellows, and students alike.

A hands-on series of instructional lectures is presented with emphasis on working through real problems.

Assessment: Graduate students taking this course select their "pet protein" based on their research projects and solve these problems using that protein. Assessment is based upon a student's protein annotation developed during the course which describes features of their protein deciphered using a variety of Internet resources. Course assignments are written using Bioeditor.


Prerequisites: None

Pharm/Bio207 is a companion course to Bioinformatics I (Pharm201). The latter provides a more in-depth and theoretical study of the material presented here and teaches the student how to build a useful database of biological data.

Course Outline

Follow links for all on-line course materials
Date Topics

Lecture 1  (Bourne) 09/30 3-5PM

  • Characterizing data resources (by currency, content, cross-linking etc.) 
  • Major data resources (e.g. Genbank, PIR, Swiss-Prot, Prosite, GDB, PDB)
  • Composite searching (e.g. ExPASy, Entrez)
  • Technical issues - plug-ins, helper applications

Lecture 2  (Bourne)10/07 3-5PM

DNA/Protein Sequence Comparison ( Backup Notes  as a PDF)
  • Similarity and homology        
  • Sequence alignments 
  • Database searches 

Lecture 3 (Bourne)10/14 3-5PM

Protein Domains and Motifs & Using BioEditor
  • BioEditor basics including rasmol and chime commands
  • Definition of domains and motifs
  • Resources providing domain and motif annotation
  • Defining your own domains and motifs

 Lecture 4 (TBN) 10/21 3-5PM


 Problem Solving with Entrez
  • Basic Sequence/Structure/Bibliographic Searching
  • Entrez field specifiers
  • Using neighbors
  • Advanced boolean searches

Lecture 5 (Bourne) 10/28 3-5PM

Protein Secondary Structure Prediction
  • Methods (Statistical, Multisequence, Neural Net)
  • Comparisons with known structure
  • Techniques

Lecture 6 (Shindyalov) 11/04 3-5PM

Phylogenetic trees
  • Principle of maximum parsimony
  • Distance methods: UPGMA, neighbor-joining
  • Multiple sequence alignment using ClustalW
  • Building tree using Biology WorkBench

Lecture 7 (Smith) 11/18 3-5PM 

Protein Physico-Chemical Data Analysis
  • Analytical tools for physico-chemical empirical data
  • Theoretical calculation of physico-chemical features
  • Compendiums of analytical tools

Lecture 8 (Bourne) 11/25 3-5PM

Protein Structure Classification 
  • Domains
  • Structural motifs
  • Folds

Lecture 9 (Shindyalov/Bourne) 12/02 3-5PM

Protein Tertiary Structure Prediction 
  • Comparative modelling. 
  • Fold recognition (threading). 
  • Molecular mechanics (ab initio methods).

Internet Resources

Portals (i.e., entry points to a number of useful data, tool and information resources)

Access Points to Multiple Databases

Important Databases

[See Nucleic Acids Research 2001 29(1) and the first issue of previous years for discussions of relevant biological databases]





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