MB620 Bioinformatics
University of New Haven
Instructor: Joel S. Bader

Class Information

Syllabus by Topic

• Applications
  Gene sequence, protein structure, gene function. DNA sequence analysis. Protein sequence analysis. Secondary, tertiary structure prediction. Structural biology. Cell/tissue distribution. Protein evolution.
• Algorithms
  Sequence comparison algorithms. Global alignments: Needleman-Wunsch, Smith-Waterman. Local alignments: FASTA, BLAST. Multiple alignments, assembly algorithms. Pattern recognition algorithms. Motifs, scoring matrices, hidden Markov models, motif generation. Clustering: distance metrics, phylogenetic trees.
• Information systems
  The Internet. E-mail. HTML. Building a web page. Databases. Relational databases. SQL. Web interfaces. Storing and retrieving information. On-line databases.
• Genomics
  The Human Genome Project: genetic maps, physical maps, sequence. Genome sequencing, EST sequencing. Major centers. NCBI, NLM, GenBank. Experimental organisms. Genetic disorders. Linkage analysis, positional cloning. Multigenic disorders. Intellectual property. The post-genome age.

Syllabus by Class

• Class 1, Apr 6 [applications]
  Sequence analysis tools. Sequence similarity searching. BLAST. Iterated BLAST. BLASTN, BLASTX, BLASTP, TBLASTN. Gapped BLAST. FASTA.
• Class 2, Apr 13 [algorithms]
  Sequence comparison algorithms. How does BLAST work?
• Class 3, Apr 20 [information systems]
  E-mail, HTML, web authoring.
• Class 4, Apr 27 [information systems]
  Web interfaces. CGIs. Using existing CGIs.
• Class 5, May 4 [genomics]
  DNA and Protein sequence databases
• Class 6, May 11 [genomics, algorithms]
  Reference sequences. Structure databases. Sequence assembly.
• Class 7, May 18 [genomics, applications]
  Physical and genetic maps. Genome sequencing. Genefinding tools.
• Class 8, May 25[algorithms]
  ORFs. Sequence similarity searching. Local and global alignments. Multiple alignments. Protein predictive methods.
• Class 9, Jun 1 [applications, algorithms]
  Protein annotation. Sequence similarity searching. Multiple sequence alignments. Phylogenetics.
• Class 10, Jun 8 [applications, algorithms]
  Inside blast.
• Class 11, Jun 15 [applications, algorithms, genomics]
  Domains, motifs, patterns. Position-sensitive scoring matrices. HMMs. Cellular localization. Secondary and Tertiary structure prediction. Fold taxonomy.
• Class 12, Jun 22 [genomics]
  Recent developments. Functional genomics. Proteomics. SNPs. Grab-bag.
• Class 13, Jun 29
  In-class final.