What: Introduction to Sequence analysis via computer
When: MWF 8:30-9:30 AM
Where: MAC/DOS Labs 4th Floor Library Admin

3 hours credit
10 students maximum

This course will introduce students to the process of
sequence analysis via computer methods. Sequence analysis in the
class will focus on software produced by Genetics Computer
Group(GCG), the EMBOSS software (EMBOSS-Peter Rice/EMBL),
ATLAS (National Biomedical Research Foundation-PIR), BLAST,
Entrez, DNA Strider,Sequencher, OLIGO and a wide range of
Internet-based sequence analysis services (such as
Indiana Univ-GOPHER; EMBL SRS; OMIM, ENSEMBLE). Students will learn to
make use of command line (text oriented), X-window (eg GCG's SeqLab)
and WWW-forms based (eg WWW2GCG and GCG's SeqWeb)access to
the software.

The general outline of the course will be to begin with
sequence entry and proceed through a series of analyses to the
point of submitting a fully documented gene to the GenBank
archive. The course will include, but not necessarily be limited
to the following topics:

Sequence entry
Archived sequence location and retrieval
Restriction Enzyme Mapping
Primer design
Fragment Assembly into contigs
Coding region location
Transcription factor binding site/Promoter location
Translation
Protein secondary structure predictions
RNA folding
Rapid Database searching
Multiple Sequence Alignment
General pattern location
On-line Mendelian Inheritance in Man (OMIM) use
Dataset creation and use
Prosite/motifs searching
Profile searching
Collating information for filling out annotated gene entry forms.

There are no prerequisites except a need for an introduction
and a desire to learn a variety of methods for sequence analysis.
The course will begin with basics of Internet usage (TELNET, FTP,
WWW Browsers-Netscape/Internet-Explorer, X-server software)
and the UNIX operating system. The main body of the course will consist
of a series of two or three lectures and one hour of hands-on
"lab" work per week. Students will be required to work through a
weekly series of exercises and propose, prepare and present to
the rest of the class, a semester project relevant to their
research interests. Grades will be based on class participation,
exercise completion and the semester project report.