"in silico DNA, RNA, Protein Sequence,
and Structure Analysis:

Theory and Practice"

Tuesday, 7 January 1997

Morning Lectures

9:30 AM Contigs, Libraries, and Restriction Fragments: Combinatorial versus Graph Theoretical Basis of Restriction Mapping and Sequencing

"Restriction Mapping: The Middle Level Problem in Genomics"

Between genetic mapping in the traditional sense of assigning chromosomal locations to loci for particular polypeptides and the the level of complete nucleotide sequences, there is a need for a middle level of physical mapping. Can we completely order restriction fragments to cover a whole chromosome? Can we do this without knowing the exact lengths of each of the fragments or what loci they contain? Interval graphs and an associated piece of software that we have developed (BENZER) will be introduced so that a qualitative approach (topological) can be understood to this important problem. Even if you have very good quantitative information, in the last analysis, a determination of whether fragments overlap one another is necessary to understand the ordering of fragments. Several other software packages have also adopted the interval graph approach and will be introduced. Other molecular biological applications of interval graphs include sequencing, complementation mappping, and deletion mapping.


10:45 AM Break

11:15 AM Evolutionary Homology versus Sequence Similarity: Darwin to DNA; Combinatorics of Sequence Comparisons, Dot Plots, Two-way and Multiple Sequence Alignments; Gap penalties; Assumptions about mutations - transition versus transversion frequencies

"Sequence Alignment"

"Similarity is observed; Homology is inferred." How is sequence similarity measured? How do different kinds of "yardsticks" influence our inferences about similarity (parsimony, maximum likelihood, and tree assmuptions? Do we employ chemical similarity of amino acyl residues or genetic similarity of notations as criteria? How much do we penalize for gaps? What can be inferred about function from sequence similarity?


12:30PM - 2PM Lunch

Afternoon Laboratories

2 PM Restriction sites, Restriction maps, Profile Analysis and Primer Design. Dot Plots, searching for similar sequences, and binary and Multiple Sequence Alignments.

SOFTWARE: BLAST (web), Dotty Plot (Mac), Benzer (Dos), Primer2.2 (web).

3:30 PM Break

3:45 - 5 PMContinuation of the early afternoon session expanded to include other programs that do similiar things.

SOFTWARE: BLITZ (web), FASTA (web), ScanProsite/ProfileScan (web), SeqPup (MacOS, Windows, UNIX), Progress Sequence Alignment (UNIX), Codon Usage (web), RecMap1.0 (Windows [restriction map program]), tacg (Unix, web [finds restriction sites]), PrimerDesign1.04 (Dos), PrimerCheck (Dos).



Description: BENZER (version 4.10) is a PC program that allows the molecular biologist to simply declare whether any two restriction fragments overlap or not, in a pairwise fashion, and from this information generate a map which satisfies these constraints.

Written by: Vince Strief (University of Wisconsin) & John R. Jungck (Beloit College)

For more information: Contact John R. Jungck


Description: A biological sequence editor and analysis program for the Macintosh, MS-Windows and UNIX platforms. It includes links to network services and external analysis programs.

Written by: Don Gilbert (Indiana University)

For more information: SeqPup readme

RecMap 1.0

Description: A MS-Windows utility for drawing restriction maps. This is a shareware version and as such is limited to only 20kb DNA segments and only 10 restriction enzymes.

Written by: Andreas Becker (University of Marburg, Germany)

For more information: RecMap readme


Description: A UNIX utility for the quick identification of restriction sites in your sequence.

Written by: Harry Mangalam (University of California, Irvine)

For more information: tacg homepage

WWWtacg Submission Form


Description: A DOS program to assist in selecting primers for PCR or oligonucleotide probes.

Written by: Andreas Becker & Joerg Napiwotzki (University of Marburg, Germany)

For more information: PrimerDesign readme


Description: A free DOS program to calculate physical (% content, annealing temperature, MW) of your PCR or oligonucleotide probes.

Written by: Andreas Becker (University of Marburg, Germany)

For more information: PrimerCheck readme


Description: A Macintosh tool for drawing dot matrix comparisons of sequences in molecular biology.

Written by: Don Gilbert (Indiana University)

For more information: DottyPlot readme


Scan your sequence for PROSITE patterns

Search you pattern against SWISS-Prot

Sequence Translation/Codon Usage

Find a primer (text or graphic output)

Design PCR primers

Primer v2.2 (text or graphic output)

NCBI (Genbank) BLAST Sequence Searching

EBI (EMBL) BLITZ Sequence Searching

EBI (EMBL) FASTA Sequence Searching

How to keep up with the literature:

Medline Searches. To use, you must first register with Medscape.

Where to find your favorite journals:

Journal of Biological Chemistry
Protein Science

BioMed Net Links to all your favorite journals: Structure, Current Biology, Current Opinion in (Biotech, Cell Bio, Immuno, Neuro), Development, etc. It is a free service (once you register), however it will only provide tables of contents and abstracts UNLESS you want to pay!

Bibliography - Restriction Mapping: Interval Graphs

Jungck, John R. and Streif, Vince. 1986. "Deletion Mapping of Genetic 'Fine Structure': Supplementing Ad Hoc Problem Solving Approaches with Algorithms and Heuristics." Midwest Bioscene 12(2):-17.

Streif, Vince and Jungck, John R. 1982. "Benzer Problem Generator." Version 4.12 Alpha (November).

Mundt, M., Faber, V., Goldberg, M., Rivenburg, R., Soderlund, C. and Torney, D. "Interval Graphs and Interactive Graphics for Resolving Ambiguities in Overlap Data." Computing and Communications Group, Los Alamos National laboratory, Los Alamos, NM 87545.

Engle, M. L., Soderlund, C. A., Stolorz, P. E., and Burks, C. "Exploring DNA Fragment Assembly Problems: Benchmarks and Stochastic Solutions." Theoretical Biology and Biophysics Group (T-10, MS K710) Los Alamos National Laboratory, Los Alamos, NM 87545.

DIMACS 1994-97 Special Year on Molecular Biology.

About SIGMA: "System for Integrated Genome Map Assembly."

Setubal, Jočo C. and Meidanis, Jočo. 1997. Introduction to Computational Molecular Biology. Table of Contents. PWS Publishing Company. 320 pp.

Murray, Darrel L. "How to Construct a Restriction Map."


Bibliography - Sequence Alignment

Feng, D.F., Johnson, M.S., and Doolittle, R.F. 1985. "Aligning Amino Acid Sequences: Comparison of Commonly Used Methods." J. Mol. Evol. 21:12-125.

Feng, Da-Fei and Doolittle, Russell F. 1987. "Progressive Sequence Alignment as a Prerequisite to Correct Phylogenetic Trees." J. Mol. Evol. 25:351-360.

Doolittle, Russell F. and Feng, Da-Fei. 1990. "Nearest Neighbor Procedure for Relatinng Progressively Aligned Amino Acid Sequences." Methods in Enzymology, 183:659-669.

Feng, Da-Fei and Doolittle, Russell F. 1990. "Progressive Alignment and Phylogenetic Tree Construction of Protein Sequences." Methods in Enzymology, 183:375-389.

Feng, Da-Fei and Doolittle, Russell F. 1996. "Progressive Alignment of Amino Acid Sequences and Construction of Phylogenetic Trees from Them." Methods in Enzymology, 66:368-381.

Programs available by Anonymous ftp: juno.ucsd.edu


Last modified: Wed Jan 1 09:19:36 1997