Course Outline

Electronic Sequence Information

Introduction to sequence formats, including multiple sequence formats
Using sequences on different platforms, including Unix
Conversion between formats using READSEQ
Using ENTREZ to obtain sequence information
Refseqs and Nomenclature

Sequence Comparisons: Pairwise

DNA vs. Protein searches (BLAST programs)
Methods: Dot Matrix Analysis; Dynamic Programming; k-tuple Methods
Programs: BLAST, BLAST2; FASTA
Scoring Matrices: PAM, BLOSUM
Profile and pattern searches: PSI-BLAST, PHI-BLAST, PROBE

Sequence Comparisons: Multiple Sequence Alignments

Methods: Dynamic Programming; Progressive; Iterative (Genetic Algorithm, HMM)
Programs: CLUSTALW
Profile analysis
Pattern searching
Visualizing & editing multiple alignments

Gene Prediction

Gene structure – prokaryotic vs. eukaryotic
Methods – Neural Networks, Pattern Discrimination
Promoter prediction

Sequence Variation

SNPs – SNP Consortium
Disease – OMIM

Genome Analysis

Automated sequencing and contig construction (Phred)
Survey of genomes – prokaryotic vs. eukaryotic
Resources: ENSEMBL; NCBI; UCSC; TIGR
Chromosome browsers
Gene Families
Homologous genes (HomoloGene, COG)
Comparative genome analysis (PipMaker, MUMmer)

Protein Classification & Structural Analysis

Protein Structure Review
Protein Sequence Databases
Protein Classification Databases
Secondary Structure Prediction
3D Structure Databases (PDB) and Resources (Chime, Cn3D)
Structural Alignments – DP, distance matrix
3D Structural Prediction

Proteomics

2D-PAGE
Kinetic Modeling: Gepasi, Virtual Cell
Mass Spec Resources
Pathway Databases: WIT, KEGG

Phylogenetic Analysis

Relation to MSA
Evolutionary trees – rooted vs. unrooted
Historical evolutionary input for tree creation
Methods: Maximum Parsimony; Distance Methods (Fitch & Margoliash, Neighbor-Joining, Unweighted Pair Group)
Programs: PHYLIP, PAUP