"Using Computers in Molecular Biology"

Instructor: Dr. Stuart Brown,

Associate Professor, NYUMC Dept. of Cell Biology

Schedule

Lectures: Mondays Feb. 11-May 6, 2-3:30 PM,
Skirball 3rd floor Seminar Room
Computer Lab: (following lectures) 3:30-5:30 PM,
Carlisle Computer Classroom (Ehrman Library)

[Course Notes (old)]
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This is a practical course in Molecular Biology Computing which will emphasize how to use the computer as a tool for research. Prerequsites include a thorough understanding of theoretical and practical aspects of molecular biology, and some University level mathematics and statistics, but no prior knowledge of computer programming or computer hardware is necessary.

Spring 2002 Course Syllabus (G16.2604):


Mon, Feb. 11
Lecture 1. Introduction to the course

Lecture 1 PowerPoint slides
Exercise for Lecture 1
  • Overview of the challenges of Molecular Biology Computing
  • The Biologist in the Age of Information and the Computer Savvy Biologist
  • Using the Molecular Biology Computing Tools at NYU Medical Center
  • UNIX, Mac/Windows, and Web Browsers as Platforms for Sequence Analysis
  • Genomics

Mon, Feb. 18
No class - President's Day

Mon, Feb 25
Lecture 2. UNIX Basics, Part I.

Reading
Why Biologists Want to Program Computers by James Tisdall
Lecture 2 PowerPoint slides
Exercise for Lecture 2
  • Logging in to the RCR Alpha
  • UNIX filenames and file protections
  • UNIX commands for working with directories
  • File transfer with FTP

Mon, March 4
Lecture 3. UNIX Basics, Part II.

Reading
How Perl Saved the Human Genome Project by Lincoln Stein
Emacs Reference Guide
Lecture 3 PowerPoint slides
Exercise for Lecture 3
  • Editing text files
  • Additional UNIX commands
  • Simple shell scripts
  • How to become a UNIX power user

Mon, March 11
Lecture 4. Finding Sequences by Name, Accession#, Keyword, or by Association

Lecture 4 PowerPoint slides
Exercise 1 for Lecture 4
Exercise 2 for Lecture 4
  • Using LOOKUP to find sequences based on keywords & phrases
  • Using ENTREZ to find and retrieve sequences and MEDLINE references
  • Using FETCH and NETFETCH to grab individual sequences or whole groups of sequences from a database
  • Genome databases
  • Other genetic databases: mutations, SNPs, etc
  • Searching the WWW for Specific Information (guest lecture by Ehrman Medical Librarian)

Mon, March 18
Lecture 5. Database Searching by Similarity

Exercise for Lecture 5
Lecture 5 PowerPoint slides
Reading:
Similarity Searching on the Web
Advanced Similarity Searching on the Web
Using Blast on the Web
Searching Sequence Databases
  • Worldwide databases
  • Similarity vs. homology
  • BLAST vs FASTA
  • Interpretation of results
  • Translation, Filtering, and other options

Mon, March 25
Lecture 6. Sequence Comparison and Multiple Alignment

Reading:
Multiple Alignment on the Web
Exercise for Lecture 6
Lecture 6 PowerPoint slides
  • Multiple Alignment: A Computational Challenge
  • PILEUP
  • CLUSTAL
  • Editing Alignments, Consensus Sequences
  • Producing Publication-Quality Printouts

Mon, April 1
Lecture 7. Sequence-Function Relationships

Exercise for Lecture 7
Lecture 7 PowerPoint slides
  • Sequence Homology and Conserved Regions
  • Conserved DNA sequences: Promoters, restriction sites
  • Combinatorial complexity of simple patterns
  • RNA Folding Patterns
  • Protein Motifs (domains)
  • GCG pattern recognition tools: FINDPATTERNS, MOTIFS, PROFILESCAN, MEME
  • Other pattern recognition software

Mon, April 8
Lecture 8. Alternate Interfaces for Bioinformatics programs

Reading:
Get Your Bioinformatics on the Web
Lecture 7 Web Pages
Exercise for Lecture 6 (SeqLab Tutorial)
SeqWeb Tutorial
  • SeqWeb: a Web interface to GCG
  • SeqLab: an X-Windows interface to GCG
  • Other Web-based Bioinformatics platforms (free and commercial)


Mon, April 15
Lecture 9. Computing Evolution: Phylogenetic Analysis

Lecture 9 PowerPoint slides
Phylogenetics Exercise
  • Sequence-based taxonomy: Overview and Assumptions
  • From Multiple Alignment to Phylogeny
    • Neighbor Joining
    • Maximum Likelyhood vs. Parsimony
  • Computer Tools for phylogenetic analysis
    • DISTANCES
    • GROWTREE
    • PAUP
    • PHYLIP

Mon, April 22
Lecture 10. Computer Tools for Sequencing Projects, PCR and Restriction Mapping

Lecture 10 PowerPoint slides
Map and PCR primer Exercise
  • Practical and theoretical problems in sequencing and assembly of contigs
  • The GCG FRAGMENT ASSEMBLY tools for managing sequencing projects
  • Using Mac/Windows desktop MolBio programs
  • The challenges of whole genome sequencing
  • Restriction Mapping WITH GCG: MAP, MAPPLOT, MAPSORT
  • Web-based tools for restriction mapping
  • PCR primer design
  • GCG tools: PRIME and FINDPATTERNS
  • Primer design tools on the web
  • DNA sequencing and fragments assembly tools
    • Sequencher
    • Consed

Mon, April 29
Lecture 11. Genomics

Readings

Mon, May 6
Lecture 12. Analysis of Microarray Data

Lecture 12 PowerPoint slides

Reading:
Gene Expression Data Analysis

  • Basics of designing a microarray
  • Image analysis
  • Normalization
  • Variability and replication
  • Clustering
  • Microarray Databases

Thursday May 23
Poster/project presentations
In the atrium by the goldfish pond.