Syllabus

1. Basic Computer skills. Jan. 19 or 21

A. Basic PC and Mac operation.
B. Logging on and off.
C. The Pine e-mail system.
D. Unix directory structure.
E. Basic Unix file handling commands.
F. The Common Desktop Environment - A graphic user interface to Unix.

2. File transfer and editing. Jan. 26 or 28

 A. The File transfer with Netscape
B. The pico editor.
C. The ex editor.
D. The vi editor.
F. The CDE text editor

 

 3. Advanced Unix file handling and job control commands. Feb. 2 or 4

A. Wildcards.
B. Job control commands.

 4. Sequences and databases. Feb. 9 or 11

 A. GCG Format.
B. The GCG programs, Fetch and Typedata.
C. The NCBI program Fastacmd.
D. GCG Tutorial Chapters 1-3 & 5.
E. Seqlab he X-windows graphic user interface to GCG
F. The NCBI Entrez web-site.

5. Comparison of Sequences. Feb. 16 or 18

 A. Graphical sequence comparison (Compare, Dotplot).(GCG Tutorial 7.1).
B. Needleman-Wunsch global sequence alignment (Gap).
C. Smith-Waterman local sequence alignment. GCG program (Bestfit) (GCG Tutorial 7.2).
D.Translation to Fasta format: Tofasta.
E. Statistical significance of local sequence alignment by random shuffling (the Fasta3 package program Prss).
F. Comparing a DNA sequence with a protein sequence - Framealign.

6. Database searching by sequence. Feb. 23 or 25

  • A. Use of the Blast World-Wide-Web interface.
    B. Interpretation of results, Karlin-Altschul theory and statistical significance
    C. The Blast algorithm.
    D. Filtering of low-complexity and repetitive sequences - Seg and Dust.
    E. The Blast family of programs (GCG Tutorial Chap. 4.2).
    F. The Fasta Family of Programs (GCG Tutorial Chapter 4.1
    •

    Catch up on lab 6. Mar. 1 or 3

    7. Database searching by keyword and motif. Mar. 8 or 9

    A. GCG Lookup.
    B. Stringsearch (GCG Tutorial chapter 6).
    C. NCBI WWW Entrez Server.
    D. Motifs (GCG Tutorial Chapter 10).
    E. The Prosite database.
    F. Searching for your own patterns. Findpatterns (GCG Tutorial chapter 6).
    G. Combining motif and full sequences searches: Phiblast.

    (No class Mar. 15 or 17 because of Spring Break)

    8. Multiple sequence alignment. Mar. 22 or 24

  • A. Progressive pair-wise alignment. Pileup (GCG Tutorial 7.3).
    B. Evolutionarily-weighted progressive pairwise alignment: Clustalw.
    C. Rigorous simultaneous multiple sequence alignment: Msa.
    D. Display of multiple sequence alignments: Pretty and Prettybox.
    •

    9. Profile methods of identifying distant homologs. Mar. 29 or 30

    A. Simple Gribskov Profiles in GCG
    A1. Introduction to profiles.
    A2. Generating profiles. Profilemake.
    A3. Comparing profiles to sequences. Profilegap.
    A4. Searching a sequence database with a profile query sequence. Profilesearch and Profilesegments.
    A5. Searching a profile database with a sequence query Profilescan.

    B. Automated profile searching: Psiblast.
    C. The Expasy web server for generalized profiles.
    D. Searching with a sets of short Profiles: Meme and Motifscan.

    10. Mapping and Primer design. Apr. 5 or 7

    A. Mapping (GCG tutorial Chapter 8).
    Restriction enzyme selection and depiction, using Map, Mapsort, Maplot, and Plasmidmap.
    B. Primer design:
    A1. Thermodynamics of DNA melting.
    A2. Primer design: Prime.
    A3. Degenerate Primers: Backtranslate

    C. Vecscreen

    11. GenomicAnalysis. Apr. 12 or 14

  • A. Filtering of repetitive sequences using Repeatmasker.
    B. Exon and gene identification: Genscan.
    C. Exon and gene identification: The Fgene web-site.
    D. Promoter identification. Pppn web-site.
    E. The Transfac databases.
    F. Transcription factor identification in the Transfac databases with Findpatterns.
    G. Identifying Transfac Profiles with Matinspector.
    •

    12. Protein secondary structure analysis. Apr. 19 or 28

    A. Pepplot, Peptidestructure and Plotstructure. These programs include the following methods:
    A1. Introduction to protein secondary structure.
    A2. The Chou-Fasman secondary structure prediction method.
    A3. Kyte-Doolittle hydrophobicity.
    A4. Karplus-Schulz flexibility.

    B. The PHD Web server.

    B1. Secondary structure prediction of water-soluble proteins.
    B2. Secondary structure prediction of membrane proteins.

    C. Signal Peptide identification- SignalP web server.
    D. Coiled-Coiled regions - Coilscan.
    E. Subcellular location (the Psort2 web server).
    F. Globularity analysis with Seg.

    (No class Apr. 21 or 26 because of Passover)

    13. Molecular Evolution. (Optional) May 3

    A. Molecular evolutionary trees: Rooted and Unrooted.
    B. Newick notation.
    C. Mutational basis of molecular evolution.
    D. Protein vs. nucleic acid methods.
    E. Distance Methods - Pileup and Clustalw.
    F. The maximum likelihood method - PROTML.
    G. Statistical significance of evolutionary trees.