I. Introduction
A. What are Bioinformatics and Scientific Computing?
C. Definitions and Concepts
1. Review of molecular biology
a. Frequencies and abbreviations for amino acids
b. Reading protein and DNA sequences correctly
2. Computer applications to molecular biology
D. Uses of Bioinformatics
1. Single sequences or genes
F. Major Genetic Databases and Access Tools
1. National Center for Biotechnology Information (NCBI)
i. Organisms and types of data stored
ii. Organization of the data, accession numbers
iii. Understanding a GenBank entry
b. Entrez to search across databases
c. PubMed literature research
ii. Searching using fields
iii. Searching using limits
d. BLAST searching programs for DNA and protein sequences
e. Online Mendelian Inheritance in Man
f. Other NCBI databases and tools
2. Other Nucleotide Sequence Databases and Software
a. Additional NCBI databases and software
b. Internet sites around the world
3. Other Protein Databases and Software
a. Additional NCBI databases and software
b. Internet sites around the world
II. Analyzing One Sequence
1. Detecting Vector Contamination
3. Analyzing DNA/RNA composition
i. Basic statistics and probability
ii. Counting words and repeats
iii. GC content: percentage of Guanine and Cytosine nucleotides
4. Finding Protein Coding Regions
1. Predicting physical properties
III. Searching for Similar Sequences
A. Homology, similarity, and identity concepts
B. The BLAST family of programs for nucleotides and proteins
3. Bit scores and E-values
IV. Alignment and Comparison of Two Sequences
3. Manual evaluation and tweaking
C. Local and Global Alignments
V. Selection, Alignment and Comparison of Multiple Sequences
A. Selecting Sequences to align
1. How many to align at once
3. Evaluating quality of and interpreting alignments
B. Clustal family of alignment programs
1. Progressive alignment is influenced by order of sequence
entry
c. Gap-extension penalties
C. Other alignment programs
D. Phylogenetic Trees for Comparison of Multiple Sequences
2. Construction Algorithms
3. Validation using Bootstrapping
E. Editing and Publishing Alignments
1. Formatting and converting data formats
2. Preparing a Multiple Alignment for Publication
3. Adding colors, shading, and logos
VI. Microarrays for Gene Expression Analysis
A. Target selection and experimental design
C. Data validation and normalization
VII. Scientific Computing
1. Creating, editing, saving, and retrieving data files
2. Converting data files to different file formats
a. Operating system file formats
b. FASTA (Fast-All) and other sequence file formats
1. Creating scientific reports
a. Text layouts and headings
2. Creating forms for scientific or lab use
1. Bioinformatic data computation and statistical analysis
2. Editing rows and columns, entering calculation formulas
3. Converting microarray or other bioinformatics data to graphs
1. Searching and retrieval in major online databases
2. Organizing lab data for local storage and retrieval
3. Organizing lab data for submission to online databases
E. Web Page Development and Searching
1. Effective scientific web page design
2. Uploading web pages to a server
3. Using Internet search engines to locate scientific
information
4. Evaluating integrity of websites
1. Effective use of email
2. Professional etiquette
3. Attaching files to emails
G. Privacy, Safety, and Security
1. Downloading files - size issues
2. Privacy and security issues
H. Introduction to Unix/Linux
1. Unix file system commands
2. Uploading and downloading files
3. Running local and/or remote bioinformatics programs
4. Introduction to scripting
1. Copyrights and infringement
2. Professional responsibility and integrity
3. Obligation to protect data
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