Practical Applications of Sequence Analysis

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Practical Applications of Sequence Analysis

• MIC 753 - The Theory and Application of Sequence
  Analysis

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Instructor (Me)

• Elliot Lefkowitz
• Office BBRB 277A
• Phone 4-1946
• E-mail ElliotL_at_uab.edu

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Time and Place

• April 3 to June 5 2001
• no class May 17
• no class May 29
• Tuesdays 300 430
• Thursdays 100 230
• BBRB 170

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World-Wide-Web Site

• http//genome.microbio.uab.edu/MIC753
• General Information
• Handouts
• Lecture Notes
• Discussion List
• Links

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Discussion List

• Talk with Elliot
• Ask questions
• Get answers
• Express your frustration
• Public!

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Email

• ElliotL_at_uab.edu
• Talk with Elliot
• Ask questions
• Get answers
• Express your frustration
• Private!
• Send me your Email Address!!

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Sequence analysis at UAB

• http//genome.microbio.uab.edu
• Many local sites mentioned in this course have
  links from this page

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Course Content

• Tools for Sequence Analysis
• GCG
• NCBI
• Databases
• Other Web-based tools
• Specialized Software
• Publication
• Understanding their use

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GCGGenetics Computer Group

• The Wisconsin Package
• Complete package of programs for sequence
  analysis
• Nucleic acid and Protein databases
• Supporting databases

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GCG Costs

• Program and database costs are subsidized by
• UAB Health Services Foundation
• UAB AIDS Center

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GCG Interfaces

• Command line
• Text based commands
• UNIX
• Graphics display
• SeqLab
• Xwindows
• Windows environment
• SeqWeb
• Web-based sequence analysis

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Other Useful Programs

• Available for
• Macintosh
• Windows PCs
• UNIX Workstations
• Web-based tools

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Microcomputer Sequence Analysis Packages

• Macintosh and IBM

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Pros and Cons

• Initially expensive
• Databases supplied on CD-ROM
• Available on-line from Genbank
• Packages vary in completeness
• Generally easy to use

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Reference Material
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GCG Documentation

• Web-based
• http//genome.microbio.uab.edu/GCG/GCG10/gcgmanual
  .html
• Username gcg
• Password uab
• Order from GCG
• http//www.gcg.com/ordering/orderdocform.html
• UNIX documentation

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GCG Users Guide

• GCG Manual Version 10.1
• Basic guide to UNIX
• Running GCG programs
• Program descriptions
• Working with data
• Generating graphics

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GCG Program Manual

• Complete Program Guide
• Description
• Input
• Output
• Parameters
• Algorithms
• Example

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SeqLab Users Guide and Tutorial

• GCG XWindows Interface
• Windows-like control
• menus
• dialog boxes
• mouse control

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SeqWeb Interface

• http//gcg.genome.uab.edu
• Flat-file version
• http//gcg.genome.uab.edu90
• Relational database version
• Web-based access to GCG programs
• Online help

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Sequence Analysis Texts
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A Practical Guide to the Analysis of Genes and
Proteins

•  Strongly Recommended
• Editors
• Andreas Baxevanis
• B.F.Francis Ouellette
• John Wiley Sons, 1998

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Sequence, Structure, and Databanks A Practical
Approach

• Editors
• Des Higgins
• Willie Taylor
• Oxford Univ Press, 2000

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Sequence Analysis Primer

• Editors
• Michael Gribskov
• John Devereux
• Groves Press, 1991

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Sequence Analysis in Molecular Biology

• Gunnar von Heijne, Editor
• Academic Press, 1987

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Phylogenetic Analysis Texts
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Molecular Systematics

• David M. Hillis and Craig Moritz (eds.)
• Sinauer Associates, 1990

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MacClade

• Analysis of Phylogeny and Character Evolution
• Wayne P. Maddison and David R. Maddison
• Program and Manual
• Sinauer Associates, 1992

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PAUP 4.0

• Phylogenetic Analysis Using Parsimony
• David L. Swofford
• Program and Manual
• Mac
• PC (DOS)
• UNIX
• Sinauer Associates, 1998
• Available later this year

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Molecular Evolution

• Computer Analysis of Protein and Nucleic Acid
  Sequences
• Methods in Enzymology, Vol. 183, Doolittle, R.F.
  (ed.)
• Academic Press, 1990

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Lecture Schedule
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http//genome.microbio.uab.edu/MIC753/schedule.htm
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Getting Started

• Introduction Communications
• Using Computers
• UNIX
• Running GCG Programs
• Text
• Graphics
• SeqLab
• SeqWeb

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Data

• Sequence and Other Data
• SeqStore
• Genbank Services
• Sequence Editing
• Fragment Assembly
• Genbank submission

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Sequence Patterns

• Mapping
• Pattern Recognition
• Protein Analysis

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Sequence Similarities

• Sequence Comparison
• Database Searching
• Multiple Sequence Analysis
• Prediction of functional motifs
• Profile Analysis

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RNA

• Secondary Structure Prediction

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Phylogenetic Analysis

• Theory
• Application

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MicroArray Analysis

• Aubrey Hill
• Director, Bioinformatics
• UAB Comprehensive Cancer Center

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Genome Analysis

• Mapping
• Sequencing
• Analysis

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Getting some real work done

• Graphics and Publication
• Working with your results

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General Lecture Outline

• What the program does
• What the program wants
• How the program works
• How can I manipulate the program?
• What do I get in the end?

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Internet-based Tools

• What is available
• How do I find them?
• How do I use them?

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Grading
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Class Projects

• Project 1 - Preparation of Web-based
  Bioinformatic Solutions
• Project 2 - Analysis of a gene family
• Understanding
• Practice

A
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Preparation of a Web-based Bioinformatic Solution

• Each student will design a web site that
  describes online, web-based solutions that are
  available to help solve a particular
  bioinformatic problem.
• Due Date Monday, May 21

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Possible Projects

• Protein motif identification
• Protein structure prediction
• Protein Families
• RNA Secondary structure prediction
• Human genome analysis
• Mouse genome analysis
• Microbial genome analysis
• Database access and searching
• Evolutionary analysis
• Sequence assembly
• Microarray analysis

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Project 1 Guidelines

• You should have your topic approved by Elliot
  prior to beginning this project. The list below
  provides examples of bioinformatic problems that
  may be appropriate, or choose your own.
• Your web site should include links to the
  appropriate web pages along with descriptions of
  what is available and a how-to guide to provide
  on-line help in using the bioinformatic tools.
• You should also provide a review of the described
  sites that focuses on their ability to solve the
  problem at hand, and ease-of-use.
• You can utilize whatever web-creation software
  you wish. Recommendations of easy-to-use web
  design programs are Microsoft FrontPage for the
  PC and Adobe PageMill for the Macintosh.
• Up to TWO students may work on this project
  together and submit a common set of files for
  their web site.

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Analysis of a gene family

• Each student will be required to identify a
  sequence family that they will analyze in
  different ways throughout the course. Each
  student must be working on a unique set of genes.
  Elliot will approve each choice on a first-come,
  first-serve basis. So it is to your advantage to
  accomplish the following assignment as soon as
  possible.
• Due Date Monday, June 11

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Project 2 Guidleines

• Pick an interesting gene family that contains at
  least six members either in multiple species, or
  in multiple alleles.
• Email a description of the gene family to Elliot
  (ElliotL_at_uab.edu) and why you think it will be
  worthwhile to study.
• Elliot will let you know if your choice is
  satisfactory. If not, you will have to choose
  another set of genes.
• Throughout the course, you should apply the
  various analytical programs demonstrated in class
  to your gene family. It will be your decision to
  choose which programs to use in your analysis.
  Your analysis should be compressive and relevant
  to the chosen gene family.
• Prepare a short journal-type paper describing
  your work.

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Computers and Communications
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Analyze the Sun UNIX Server

• Sun E450 Server
• analyze.genome.uab.edu
• gcg.genome.uab.edu

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Analyze Accounts

• Provided to all registered students
• Feel free to experiment
• Do Not provide access to other individuals
• Username first initial last name
• elefkowitz
• Password
• Social security number

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Analyze Accounts

• Others may register for access
• http//genome.microbio.uab.edu/GCG/GCGatUAB.htm
• Username gcg
• Password uab

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Change Your Password!

• On analyze
• passwd
• SeqWeb
• Preferences
• Change password

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Run The Programs!!

• Only way to learn
• Your grade depends on it!

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Required Hardware

• Computer with a modem or ethernet connection to
  the Internet
• Macintosh
• Windows PC

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Required Software

• Web Browser
• Internet Explorer v5.0
• Netscape v4.6
• Communications Program
• Email account and client
• Send me your Email Address!

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Communications Software

• VT100 or VT220 Terminal Emulation
• Text
• Tektronix 4105 or 4014
• Graphics
• XWindows

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Macintosh

• NCSA Telnet 0
• vt100/graphics
• freeware
• VersaTerm-Pro 195
• vt100/graphics
• Synergey Software
• eXodus 149
• XWindows
• White Pine Software

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PC

• Tera Term Pro 0
• vt100/graphics
• Freeware
• SmarTerm Office 316
• vt100/graphics
• Esker Software
• WinX-32 149 (60 student license)
• XWindows
• eXodus 149
• XWindows
• White Pine Software

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Connection to analyze

• Internet Connection
• Ethernet
• Direct campus connection
• Modem
• Through ISP
• Domain name
• gcg.genome.uab.edu

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For more information

• See the web site
• http//genome.microbio.uab.edu/MIC753/

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Next Up

• Using Computers