MCCCD Official Course Competencies:

CSC283  2009 Spring – 2011 Summer II

Bioinformatics and Scientific Computing

1.

Identify major genetic databases and access tools and describe special features and strengths of each. (I)

2.

Use software to perform basic statistical analyses and characterize sequences. (II)

3.

Use software to locate open reading frames. (II)

4.

Use available software to search genetic databases for similar sequences. (III)

5.

Use available software to align sequences and determine similarities. (III, IV)

6.

Select appropriate multiple sequences, align them, and evaluate the results. (V)

7.

Construct various types of phylogenetic trees from multiple aligned sequences. (V)

8.

Perform normalization and statistical analysis on microarray gene expression data. (VI)

9.

Use a word processor to create bioinformatic reports and forms. (VII)

10.

Use a spreadsheet to perform statistical analysis and create graphs of bioinformatic data. (VII)

MCCCD Official Course Outline:

CSC283  2009 Spring – 2011 Summer II

Bioinformatics and Scientific Computing

I. Introduction

A. What are Bioinformatics and Scientific Computing?

B. History

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

E. Levels of Focus

1. Single sequences or genes

2. Domains and families

3. Metabolic pathways

4. Genomes

F. Major Genetic Databases and Access Tools

1. National Center for Biotechnology Information (NCBI)

a. GenBank database

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

i. Basic searching

ii. Searching using fields

iii. Searching using limits

iv. MeSH terminology

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

A. Nucleotide Sequences

1. Detecting Vector Contamination

2. Restriction Maps

3. Analyzing DNA/RNA composition

a. Basic statistics and probability

b. Counting words and repeats

c. GC content: percentage of Guanine and Cytosine nucleotides

d. Other analyses

e. Analysis software

4. Finding Protein Coding Regions

a. Open Reading Frames

b. Exons

c. Assembly

B. Protein Sequences

1. Predicting physical properties

2. Predicting structure

3. Finding domains

III. Searching for Similar Sequences

A. Homology, similarity, and identity concepts

B. The BLAST family of programs for nucleotides and proteins

1. Choosing parameters

2. Masking

3. Bit scores and E-values

4. Formatting output

5. Evaluating results

IV. Alignment and Comparison of Two Sequences

A. Issues

1. Sequence lengths

2. Scoring algorithms

3. Manual evaluation and tweaking

B. Dot Plots

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

2. How close in identity

3. Evaluating quality of and interpreting alignments

B. Clustal family of alignment programs

1. Progressive alignment is influenced by order of sequence entry

2. Parameter refinements

a. Substitution matrices

b. Gap-opening penalties

c. Gap-extension penalties

C. Other alignment programs

D. Phylogenetic Trees for Comparison of Multiple Sequences

1. Types of Trees

a. Binary Trees

b. Consensus Trees

c. Phylograms

2. Construction Algorithms

a. Maximum Parsimony

b. Neighbor Joining

c. Maximum Likelihood

3. Validation using Bootstrapping

VI. Microarrays for Gene Expression Analysis

A. Target selection and experimental design

B. Image analysis

C. Data validation and normalization

D. Statistical analysis

VII. Scientific Computing

A. Text Editors

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

B. Word Processing

1. Creating scientific reports

a. Text layouts and headings

b. Tables

c. Charts or graphs

d. Diagrams

2. Creating forms for scientific or lab use

C. Spreadsheets

1. Bioinformatic data computation and statistical analysis

2. Editing rows and columns, entering calculation formulas

3. Converting microarray or other bioinformatics data to graphs

D. Databases

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

F. Electronic Mail

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

3. Virus dangers

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

I. Ethics

1. Copyrights and infringement

2. Professional responsibility and integrity

3. Obligation to protect data