Power Point slides for CS6890

• Lecture One, basic problems and methods
• Lecture Two, database searching
• Lecture Three, BLAST method of searching
• Lecture Four, Multiple Sequence Alignment
• Lecture Five, Hidden Markov Models

Readings on Bioinformatics and Biology

• Basic tutorial on DNA, RNA and Proteins
• The Molecular Biology Database Collection: 2003 update -- Nucleic Acids Research 31(1):1-12
• Entrez tutorial on how to use the NCBI web site
• Lecture Notes on Dynamic Programming alignments, particularly the simple example and the more complex example
• The NCBI BLAST education pages (all three sections).
• Altschul, et al on PSI-BLAST and on improving PSI-BLAST (using ROC curves)

Readings on Machine Intelligence applications to Bioinformatics

• Review and Tutorial on AI and Bioinformatics

Database of research papers in Bioinformatics

• PubMed Journal Paper search

Terminology Sites

• Look up definitions (Incomplete)

Application Areas for Projects (to be extended)

• Learning and optimization methods for Protein Folding (Determining the 3D structure from the amino acid sequence)
• Optimization methods for multiple sequence alignment
• Modeling and representation of the development process (Morphogenesis)
• Learning techniques to recognize coding regions of DNA sequences
• Data mining techniques to identify useful drugs
• Natural language understanding systems to search abstracts for specific information