Introduction to Applied Bioinformatics

Dr. Benjamin F. Matthews
Soybean Genomics and Improvement Laboratory
United States Department of Agriculture
Beltsville, MD 20705

Course Schedule:

Lecture No.  Title

Note: click on the lecture title for pdf version of the lecture notes in color, or click the grey scale link for a black and white version (less size).

1. Introduction to Bioinformatics and Literature Searches
Overview of bioinformatics; Databases; PubMed, AGRICOLA 
(Grey scale).

2. DNA Retrieval and Similarity Searches
NCBI,ENTREZ, GenBank, GenBank files; BLAST
(Grey scale).

3. DNA editing, Pairwise Alignment and Contig Assembly
ExPASy; Phred, Phrap, Consed, ExPASy; translation
(Grey scale).

4. DNA Translation into Protein and Pairwise Alignment
ExPASyMethods of alignment, PAM, BLOSUM
(Grey scale).

5. Multiple Sequence Alignment; Motifs and Phylogenetic Trees 
Pfam, ProfileScan, ClustalW
(Grey scale).

6. DNA Restriction Analysis and Primer Design
BioTools, Restrictionmapper, WebCutter, Frodo, Primer3
(Grey scale).

7. Genome and Pathway Networks; SNP Discovery
Networks and pathways; KEGG
(Grey scale).

8. Genomic Sequence Analysis
Gene and genome Databases, GenScan, GenMark, Softberry
(Grey scale).

9. Applied Bioinformatics at the USDA
(Grey scale).

Download all lectures in zip format: In color or grey scale (smaller file size)

Last updated: 2/18/2005