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Workshops
for teachers and researchers 
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The resources used with each workshop are listed in the workshop description.
2004 Workshop Schedule
To arrange for workshop or course, contact: info@geospiza.com
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An introduction to sequence comparison using BLAST. This
workshop usually includes a short description of "what
is bioinformatics?", an overview of what BLAST does,
and a hands-on activity where participants get a sequence
from our web site, do a BLAST search, and answer questions
about the sequence.
Tutorial: BLAST for beginners
Additional materials:
BLAST worksheet
DNA sequences of "unknown origin"
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An overview of various databases at NCBI and a discussion
of strategies for finding information and determining if
what you've found is what you were looking for. Participants
brainstorm to identify genes of interest in plants and
then use various strategies to find them in GenBank.
handouts:
instructor version 
student
version
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This covers using NCBI's LocusLink and Genes and Disease
to research different aspects of an inherited disease.
Participants find information about Lou Gehrig's disease,
use OMIM to find a list of alleles, and use Cn3D to identify
where the mutations are located in the three dimensional
structure of the enzyme superoxide dismutase, with the
goal of trying to develop
a hypothesis to explain why a particular amino acid change,
affects the activity of the enzyme.
Tutorial: Allelic Variants of Human Superoxide Dismutase
Additional materials: SOD Variant worksheet
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Structure-viewing applications like Cn3D, RasMol, MAGE, and
Chime, can help students visualize and understand differences
between macromolecules like proteins and nucleic acids. The
application used in this workshop, Cn3D, is is freely available
from the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov)
and easy to use.
In this workshop, participants will use Cn3D to examine and
distinguish between, the primary, secondary, and quaternary
levels of protein structure and to compare the structures
of proteins and nucleic acids.
Tutorial: Introduction to Protein Structure
Additional materials:
Amino acid abbreviations ( 24kb)
Amino acid structures (36kb)
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Mitochondrial DNA sequences are widely used as tools for
identifying maternal ancestors and
studying human migration. Workshop participants use mitochondrial
sequences from different regions of the world to determine
if they can confirm the origin of these sequences, and then
identify the maternal origin of an unknown sequence.
Tutorial: Mitochondria
and Chloroplasts - maternal inheritance
Additional materials:
Maternal inheritance worksheet
Maternal sequences of unknown origin
Maternal Inheritance
Answer Key - available at workshops
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Mitochondria and chloroplasts have their own genomes and
exist independently inside the cell.
The small size of their genomes and the limited number of
proteins make them an excellent model for studying genomic
biology. Workshop participants will review some facts about
these organelles, come up with study questions, determine
which questions can be answered with bioinformatics tools,
and then use different types of bioinformatics tools to research
the
answers.
Tutorial: Mitochondria and Chloroplasts
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Single nucleotide polymorphisms, or SNPs, are responsible
for most of the individual differences
within a population. An extensive effort is underway to identify
and catalog SNPs with one possible goal, the development
of better diagnostic tools and individualized medicine. However,
DNA sequencing is not error-free. How do we distinguish between
a polymorphism and a sequencing mistake?
This workshop discusses some of the bioinformatics tools
used in DNA sequencing and assembly, such as phred and phrap,
and some strategies for discovering new SNPs.
Workshop participants use bioinformatics tools to determine
if sequencing discrepancies are
likely to be SNPs or sequencing mistakes.
Tutorial: SNP or sequencing error?
Additional materials:
Contig
sequences and phrap quality graphs from four genes of medical importance
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Funding
for this project was provided by the National Science Foundation's
Course, Curriculum, and Laboratory Improvement Program under
grants DUE-0088153 and DUE-0127599, also from Bio-Link,
an NSF Advanced Technology Education Center.
Any
opinions, findings, and conclusions or recommendations
expressed in this material are those of the author and do
not necessarily
reflect the views of the National Science Foundation. |
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