In November, Dr Vaughn asked me to give a lecture to his cell physiology students at the University of Central Oklahoma.
This lecture centered on the uses of bioinformatics its approaches to disease. I wanted the students to be able to not only
choose a Mendelian disorder and explore its phenotype, but also to find sequence information about the gene that, when
mutated, gives rise to the gene. Also, if possible, identify the nonsynonymous mutation on a predicted 3D structure.
The students were introduced to the National Center for Biotechnology Institute (NCBI) website and several of the databases
available to them. First they learned of a literature databases called Online Mendelian Inhertance in Man (OMIM) database
that contains information on Mendelian diseases and genes. They were then shown how to obtain sequence information by
following the links to the Entrez Gene database, which is a gene centered database the provides lots of annotations for
well studied genes. They were then shown how to interpret the curated BLAST search called BLINK where they could identify
conserved domains, homologous sequences in a number of organisms, and homology to sequences with a known 3D structure.
Following this, they could then visualize the 3D structure of the protein and identify a nonsynonymous mutation in the structure
with Cn3D, NCBI's molecular visualization tool.
This past October, I had the pleasure of working with Dr. Hanson and Dr. Rundle at the University of Central Oklahoma.
They asked me to lecture to their biochemistry students and introduce them to bioinformatics. I thought it
would be a great idea to have the students be able to take an unknown amino acid sequence and identify as much as they
possibly could about its biochemistry using bioinformatics tools available on the web. Because Dr. Hanson wanted a
challenge for their students, I created a lecture and lab assignment for the students so that by the end of the class,
they would be able to do the following:
- Accurately read a sequence database record and extract pertinent information concerning its function,
domains architecture and composition, and structure, if a structure is available.
- Perform and understand global and local pairwise sequence alignments
- Search a sequence database for homologous sequences to both known and unknown sequences and accurately
interpret alignment scores.
- Identify conserved domains in unknown protein sequences by comparing them to protein signature
databases.
- Assess the evidence from sequence homology searching to assign descriptor s to unknown sequences such
as gene/protein name, function, gene ontologies, and Enzyme Commission (E.C.) numbers (if it is an enzyme).
- Predict protein physico-chemical parameters for a known or unknown sequence
- Make secondary and tertiary structure predictions
These are the types of tasks one might be asked to do when annotating a genome. The only missing step is gene prediction.
If you would like this presentation taught to your class, or something similar, please fell free to contact me at your convenience.
Dr. Jenna Hellack from University of Central Oklahoma invited me to give a lecture on bioinformatics to her evolution class over the summer. I thought it to be appropriate to expose the students to the process of building phylogenetic trees using bioinformatic tools available on the web. The website that I introduced them to was the The European Bioinformatics Institute Services website (http://www.ebi.ac.uk/services/). This site provides tools to perform global and local pairwise sequence alignments, multiple sequence alignments, phylogenetic tree building, BLAST searches against nucleic and amino acid sequences and more.
During the lecture, I first exposed to students to both global and local pairwise sequence alignment tools that are necessary for determining how closely related two sequences are. They were then exposed to the process of creating multiple sequence alignments for several homologous sequences from different organisms and also to the importance of accurate alignments for building trees. The multiple sequence alignment was then used in an example that involved building a phylogenetic tree to represent the evolutionary relationships between the organisms in the example. Lastly these students were taught how to perform their own BLAST searches to identify homologous sequences that they might want to use in their own evolutionary studies.
The students were then prepared for Dr. Hellack's project. She had the students determine the evolutionary relationships between several organisms. They would first search for homologous sequences using BLAST and then use these sequences to model the evolutionary relationships between the organisms.
If this is something you think you would like your students to be exposed to, please feel free to contact me at your convenience.
The National Center for Biotechnology Information (NCBI) is a division of the National Library
of Medicine and the national Institutes of Health, established by Congress on November 4th 1998. the purpose of NCBI is
to ''develop new information technologies to aid in the understanding of fundamental molecular and genetic processes that
control health and disease'' (NCBI mission). To help the scientific
community better understand ho to use their resources, NCBI provides a free training course, ''A Field Guide to GenBank
and NCBI Molecular Biology Resources''. NCBI sends speakers to any university to deliver a lecture and hans-on computer
sessions to expose people to their resources.
In September, Ursula Ellis (OUHSC Reference librarian) and I (OK INBRE) sponsored NCBI’s Steve Pechous
and Andrei Gabrielian to deliver this workshop in the Bird Library at OUHSC. The two-day workshop began with a three-hour
overview of several of the databases and tools currently maintained at NCBI. This lecture was followed by hands-on sessions
to give attendees an opportunity to explore the tools on the NCBI web site. The lecturers touched such issues as using Entrez,
the NCBI integrated text-based search and retrieval system, and how to effectively utilize the NCBI integrated databases to
retrieve related information stored in other databases. Practical issues also were covered, such as how one can optimize a
BLAST search by modifying the BLAST parameters.
The attendance was quite good, with 90 registrants. Faculty, staff and studetns from several institutions attended,
including OUHSC, NSU, UCO, OBU, Cameron Univ., OKCCC, OU, OSU, the Samuel Roberts Noble Foundation, and KANresearch.
For those who would like additional information about this workshop, please go to the NCBI Field Guide site.
I had the wonderful opportunity of working with Dr. K.J. Abraham at Langston University. He is interested in using DeepView (also known as Swiss-PDB Viewer
) to explore the relationship between the structure and function of several proteins in which he is interested. Deep
View is a free application that can be used to simultaneously analyze the 3D structure of several proteins. Not only does
this application give the user a wide range of visualization options for protein structures, but it also will superimpose
protein structures so that structural similarities and differences can be explored.
To help Dr. Abraham use this tool, I developed a tutorial that discussed several
issues, including the usage of some of the basic components of the software, how to superimpose protein structures, how to
identify what amino acids are drastically unaligned, how to change the representation and color of proteins to better
highlight similarities and differences.
A second interesting program called Multiple Alignment by Secondary Structures (MASS) also was of benefit. (Dror
O, Benyamini H, Nussinov R, Wolfson HJ. Multiple structural alignment by secondary structures: algorithm and
applications. Protein Sci. 2003 Nov; 12(11):2492-507.) This is a method for the structural alignment of multiple
protein molecules and the detection of common structural motifs. MASS is based on a two-level alignment, first using
secondary structure elements for aligning multiple protein structures and then atomic representation for fine-tuning.
Using this software I was able to align several of Dr. Abraham's proteins so that he could explore global structural
similarities and differences of his proteins.
If anyone has any questions or would like for me to develop similar tutorials for them, please feel free to contact me at your convenience. I've included a link to the tutorial and to some crystal structures
of human profilin to download.
I had the pleasure of working in November with Dr. Cindy Cisar and her microbiology
students at Northeastern State University in Tahlequa, OK. Dr. Cisar asked me to prepare
a bioinformatics lab for her microbiology students, to expose them to this new field.
I presented a one-hour lecture on bioinformatics, and gave the students a lab assignment
in the final hour. During the lecture I defined the term "bioinformatics" and discussed
the importance of biological databases, computational tools and the Internet to this field.
The lecture gave several examples of bioinformatics Internet resources.
The students then assembled a small bacterial plasmid from raw sequence data and predicted
genes from the assembly. To do this, the students downloaded the DNA sequence reads from the
OUHSC microgen web site . These sequences
were assembled using CAP3 , an online
sequence assembly program. The students then predicted potential open reading frames from
the assembled sequence data using NCBI's
ORF Finder . Using the translated protein sequences from ORF Finder, they then compared
two "unknown" sequences against the ExPASy site, using
the BLAST algorithm. Each student
predicted the most likely function for the unknown protein sequence and was asked to justify
their assignments. They also had to identify the scientific papers that discussed the
function of the predicted protein.
If you would like me to prepare a similar tutorial for your laboratory class, please let
me
know. The text of the tutorial that I presented can be found on our web site at
microgen.ouhsc.edu/nsu-lab/ .
Below is a list of the different schools that I have presented or will present this lab to.
| WHO and WHERE |
DATE |
TIME |
| Northeastern State University (@ NSU) |
November 23rd, 2004 |
9:00 a.m., 11:00 a.m., 2:00p.m. |
| University of Central Oklahoma (@ UCO) |
January 19th, 2005 |
4:00 p.m. |
Southwestern Oklahoma State University (@ OUHSC)
| April 15th, 2005 |
1:00 p.m. |
The OKRA project is a multi-campus research project for undergraduate students enrolled at
the INBRE undergraduate campuses. This project will give these students an invaluable experience
in bioinformatics, molecular biology and genomics. The students will experience first-hand
what it is like to analyze and understand the entire genomic complement of a microorganism,
make real-world decisions about data interpretation, explore the scientific literature in-depth,
and participate in publishing a scientific paper.
Currently, one of the most vexing problems faced by the discipline of
microbial genomics is the paucity of efforts for ongoing curation of the
existing microbial genome sequence databases. This leads to a gradual
degradation of the usefulness of this resource since no new studies are
being incorporated into this database and the scientific community thus
cannot derive its full benefit. Funding agencies have typically been reluctant
to devote resources to curation or "re-annotation" of these genome sequence
databases, once established. Re-annotation of these resources has therefore
typically been an ad hoc process, generally performed by the original
group that sequenced the genome. The process of updating these databases
has often been haphazard and non-uniform. Further, re-annotation of a
genome sequence database typically involves considerable effort but little
explicit academic reward, which acts as a disincentive.
Encouraged by the recent AAAS review of the OK BRIN project, we plan to use the potential of
microbial genome sequence re-annotation as a way to introduce Oklahoma
undergraduate students to bioinformatic analysis of genome sequence data,
and at the same time update and enhance the annotation of existing microbial
genome sequence databases. The OKRA project will be directed by Mr. Edgar Scott, our Multi-Campus
Bioinformatics Education Specialist with the support of the INBRE Bioinformatics
Core at the OUHSC. For a more detailed description of the OKRA
project, please download the pdf file.
Seminars
|
The purpose of this presentation is to expose the audience to
bioinformatics and to introduce the
Oklahoma Re-annotation Project (OKRA Project).
Bioinformatics is an interdisciplinary field that is concerned with
using computers to obtain knowledge from the analysis of stored biological
data. Through the use of databases to organize and manage biological data,
bioinformatics programs to analyze and process data, and the Internet
to share information freely, bioinformatics is a field that strives to
enable the discovery of new biological insights. It is also being
incorporated into different fields to help achieve their goals.
For example pharmacogenetics is using bioinformatics to understand
the relationship between a patient's genetic expression and drug responses
in an effort to develop more effective drugs and limit adverse drug
responses in patients. Phylogenetics uses bioinformatics to obtain a
more accurate understanding of the evolutionary relationships between
different organisms. Also medical research is currently being performed at
OUHSC to better understand and identify bacterial populations that lead to infections.
|
| WHERE |
DATE |
TIME |
Southeastern Oklahoma State University
Science Building
(building 23) , Room S-202 |
September 16th, 2004 |
6:00 p.m. |
Cameron University
Science
Complex (building 6), Room 105 |
September 24th, 2004 |
2:00 p.m. |
Langston University
Hamilton Hall, Room 205 |
October 14th, 2004 |
12:00 p.m. |
Southwestern Oklahoma State University
General Thomas P.
Stafford Center (building 15), Room 104 |
November 11th, 2004 |
7:00 p.m. |
| Oklahoma City Community College |
November 17th, 2004 |
12:00 p.m. |
Tulsa University
Oliphant Hall (building 22), Room 300 |
November 18th, 2004 |
12:30 p.m. |
| Northeastern State University |
February 2nd, 2005 |
3:00 p.m. |
|
