"Using Computers in Molecular Biology"

Instructor: Dr. Stuart Brown,

Assistant Professor, NYUMC Dept. of Cell Biology

Schedule

Lectures: Mondays Feb. 14-May 8, 1-2:30 PM,
Alumni Lecture Hall A,B and other places ... (sigh)
Computer Lab: (following lectures) 3-5 PM,
Carlisle Computer Classroom (Ehrman Library)

[Course Notes]
[Back to the RCR Homepage]

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 2000 Course Syllabus (G16.2604):


Mon, Feb. 14 (Alumni Aud. A)
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
  • Genomics

Mon, Feb. 21
Holiday, no class this week

Mon, Feb. 28 (Alumni Aud. A)
Lecture 2. UNIX Basics, Part I.

  • Logging in to the RCR Alpha
  • UNIX Filenames
  • UNIX commands for working with directories
  • UNIX file protections

Mon, March 6 (Alumni Aud. B)
Lecture 3. UNIX Basics, Part II.

  • Editing text files
  • Additional UNIX commands
  • Using graphics with GCG
  • File transfer with FTP

Mon, March 13 (MSB-248)
[NOTE ROOM CHANGE]
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 and NETFETCH to grab individual sequences or whole groups of sequences from a database

Mon, March 20 (Alumni Aud. B)
Lecture 5. Database Searching by Similarity

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

Mon, March 27 (Alumni Aud. A)
Lecture 6. Sequence Comparison and Multiple Alignment

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

Mon, April 3 (MSB-248)
[NOTE ROOM CHANGE]
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 Motifs (domains)
    • The PROSITE Database
    • The BLOCKS Database
  • GCG's pattern recognition tools: FINDPATTERNS, MOTIFS, PROFILESCAN, MEME
  • Other pattern recognition software

Mon, April 10 (Alumni Aud. A)
Lecture 8. Computer Tools for Sequencing Projects, PCR and Restriction Mapping

  • 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.

  • Restriction Mapping
    • MAP
    • MAPPLOT
    • MAPSORT
    • Web-based tools for restriction mapping
  • PCR primer design
    • Theory & physical chemistry of PCR
    • Applications of PCR technology
    • PRIME
    • FINDPATTERNS
    • Primer design tools on the web

Mon, April 17 (Alumni Aud. A)
Lecture 9. The Internet for Biologists

  • "The network is the computer." Platform independent computing.
  • E-mail: The most basic Internet function is still the most important
  • Mailing lists
  • Internet Newsgroups
  • Orgins of 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

Mon, April 24 (Alumni Aud. B)
Lecture 10. Genomics

  • What is Genomics - technology vs. philosophy
  • Bioinformatics is an essential part of Genomics
  • Genome scale sequencing
  • Comparative Genomics (evolutionary genomics)
  • ESTs and SAGE for expression mapping
  • Microarrays
  • Proteomics
  • New technologies and new bioiformatics tools
  • Genomics on the web


Mon, May 1 (Alumni Aud. B)
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
    • PAUP
    • PHYLIP

Mon, May 8 (Alumni Aud. B)
Lecture 12. Graphical Interfaces for GCG

  • SeqWeb, a web interface to GCG
  • SeqLab, an X-Windows interface to GCG
  • Integration of GCG programs