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Basic Bioinformatics: From Sequence Analysis to Genome Analysis

SOT is providing this popular 1999 Continuing Education sunrise mini-course for free. We only ask that you answer a few survey questions before and after the course.

Course Description

Presenter: William B. Mattes

Bioinformatics was born out of a need to make sense of the coded data generated after the advent of DNA sequencing. Thus molecular biology saw not only an influx of computer analyses but also a visionary approach to the explosion of information—public databases of sequence information (e.g., GenBank). This short, basic course is designed to introduce the participants to the field of bioinformatics and will provide a background, both historical and conceptual, for understanding present and future applications of this technology in toxicology. Bioinformatics will be explained as a variety of tools, encompassing nucleotide and protein sequence analysis, structure and function prediction tools, genetic linkage analysis, and database mining tools. The vast array of databases available over the web will be introduced, as well as some of the approaches that one may take to use these data in a simple fashion (e.g., retrieval of GenBank information at a number of different levels).

Technical Considerations

You may download the course in its entirety or view it online through the links below.

Full course files:

Downloading instructions:

The course downloads as a .zip archive. If you’re a Mac user, you need an unzipping utility such as MacZip or ZipIt so you can access the files. The course itself is designed to run in your web browser, whether Mac or PC. Simply open the index.htm file from within your browser, and you’re ready to go.

Table of Contents

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Basic Bioinformatics: From Sequence Analysis to Genome Analysis

Bioinformatics

Summary of Course

Overview

Why

What

How

Historical Background

Conceptual Background

Conceptual Background (cont)

Types of Algorithms

Types of Algorithms

Types of Algorithms (cont)

Types of Algorithms (cont)

Types of Algorithms (cont)

Tools—Nucleotide Sequence Analysis

Tools— Protein Sequence Analysis

Tools— General Sequence Analysis

Tools— General Sequence Analysis

Tools— General Sequence Analysis

Tools— Function Prediction

Tools— Structure Prediction

Tools— Database Mining

Software Program Sources

Database Resources

Database Resources (cont)

Getting Sequence Data

Bioinformatics Operator Basics

Bioinformatics Operator Basics (cont)

Bioinformatics Operator Basics (cont)

Simple Entrez Session

National Center for Biotechnology (NCBI) Website

Entrez Browser

Entrez Monkey Nucleotide Sequence Search

Entrez Nucleotide Query

Entrez Nucleotide Query Results

Entrez Nucleotide Query Final Result

Simple Blast Search

Entrez Mouse Nucleotide Sequence Search

Entrez Nucleotide Query

Entrez Nucleotide Query Results

Entrez Nucleotide Query Final Result

Entrez Protein Query

Entrez Protein Query Results

FASTA Protein Sequence Result

Highlight and Copy Protein Sequence Result

BLAST Search Tool

Basic BLAST Search

Paste Sequence into Basic BLAST Search

BLAST Results

BLAST Results (cont'd)

Summary

Where to get more information

Final Note