"Using Computers in Molecular Biology"

Instructor: Dr. Stuart Brown,

Assistant Professor, NYUMC Dept. of Cell Biology

Tentative Schedule

Lectures: Tuesdays Feb. 17-May 5, 1-2:30 PM,
Alumni Lecture Hall B
Computer Lab: (following lectures) 3-5 PM,
Carlisle Computer Classroom (Ehrman Library)

[Course Notes]
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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 1998 Course Syllabus (G16.2604):


Lecture 1. Introduction to the course

  • 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
  • Using a Web Browser as the Platform for Sequence Analysis

Lecture 2. The Basics of using the RCR DEC Alpha Server

  • Logging in to the RCR Alpha
  • VMS Filenames
  • Using VMS MAIL for E-mail
  • VMS NEWS

Lecture 3. More basics of using the Alpha

  • VMS commands for manipulating directories
  • File protection
  • Editing text files with EVE
  • VMS "Symbols" and "Logical names"
  • Using graphics with GCG

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

  • Using LOOKUP to find sequences based on keywords & phrases
  • Using ENTREZ to find and retrieve sequences and MEDLINE references
  • Using FETCH to grab individual sequences or whole groups of sequences from a database

Lecture 5. Database Searching by Similarity

  • Worldwide databases
  • Similarity vs. homology
  • BLAST vs FASTA
  • Interpretation of results
  • Translation, Filtering, and other options

Lecture 6. Sequence Comparison and Multiple Alignment

  • A Computational Challenge
  • PILEUP
  • CLUSTAL
  • Editing Alignments, Consensus Sequences
  • Producing Publication-Quality Printouts

Lecture 7. Sequence-Function Relationships

  • Sequence Homology and Conserved Regions
  • DNA sequence conservation:
  • Protein-coding Regions
  • Promoters
    • Transcription Factor Binding Sites (the TFSITES database)
    • Restriction Enzyme Clevage sites (the REBASE database)
  • RNA Folding Patterns
  • Protein Active Sites
    • The PROSITE Database
    • The BLOCKS Database
  • GCG's pattern recognition tools: FINDPATTERNS, MOTIFS, PROFILESCAN
  • Other pattern recognition software

Lecture 8. Using the Internet for Molecular Biology Research

  • "The network is the computer." Platform independent computing.
  • E-mail: The most basic Internet function is still the most important
  • Mailing lists
  • Internet Newsgroups
  • Gopher: What is it and why doesn't anybody talk about it anymore?
  • What is the World Wide Web?
  • Using Netscape to Surf the Web
  • Information on the WWW for Biologists
  • Searching the WWW for Specific Information
  • The future of the Internet and the WWW

Lecture 9. Restriction Maps and PCR Primers

  • MAP
  • MAPPLOT
  • MAPSORT
  • PRIME
  • FINDPATTERNS

Lecture 10. Computer Tools for Sequencing Projects

  • Practical and theoretical problems in sequencing and assembly of contigs
  • The GCG FRAGMENT ASSEMBLY tools for managing sequencing projects
  • Using SEQED, the sequence project editor of GCG
  • Sequence formats and reformatting for GCG
  • Using the Mac programs Sequencher, MacVector, and GeneWorks for sequencing projects
  • Theoretical and Practical approaches to large scale sequence assembly- Shotgun sequencing of whole genomes.

Lecture 11. Computing Evolution: Phylogenetic Analysis

  • Sequence-based taxonomy: Overview and Assumptions
  • From Multiple Alignment to Phylogeny
    • Neighbor Joining
    • Maximum Likelyhood vs. Parsimony
  • The Molecular Clock
  • Computer Tools for phylogenetic analysis
    • DISTANCES
    • GROWTREE
    • PHYLIP
    • Many, many others = An unresolved area of the science

Lecture 12. The New SeqLab Graphical Interface for GCG

  • X-Windows is a graphical interface to the DEC Alpha server
  • SeqLab Basics
  • Using SeqLab to improve the integration of GCG programs