Welcome to Biochem 920.  I hope this will be an enjoyable learning experience 
for all of you.  

Biochem 920 Bioinformatics Special Topics Course

Instructor David Nelson email dnelson@utmem1.utmem.edu

Meeting times 2:30-5PM Thursdays starting Feb. 3, 2000

Course description as posted on the UT course info pages

BIOC 920
               Special Topics in Biochemistry: Bioinformatics--Sequence
               Analysis and Sequence Databases
               D. Nelson
Day: Th Time: 2:30-5
Place: Alexander 307 in the library across from the elevator
Credits: 2
This course is a practical, computer lab course with no tests, only assignments to be 
completed to demonstrate the use of certain tools or the ability to find specific 
information. Topics include an overview of the main databases Genbank, Unigene, OMIM; 
building up a complete protein sequence from ESTs; strategic BLAST searching; finding the
intron-exon boundaries in unannotated genomic DNA, finding single nucleotide 
polymorphisms in your gene; locating your gene on a human or mouse chromosome map 
(what are the nearest neighbors or landmarks? is there a disease locus that maps near 
your gene?); finding the syntenic region of a mouse or human gene;  searching for protein 
motifs in a sequence; detecting alternative splicing by comparing genomic and EST/mRNA 
data; recognizing retained introns in ESTs (processing is not always complete); solving 
problems with automated systems like UNIGENE (errors that simple programs cannot detect); 
using ACEDB (A C. elegans database), Flybase, AthDB (Arabidopsis thaliana database), SGD 
(Saccharomyces genome database); keeping up with the genome projects and who’s doing 
the work (Washington Univ., Sanger Center, Kazusa, etc.); and blast searching data not 
yet in Genbank. Limited to 20 students. 

The class will meet on these dates: February 3, 10, 17, 25(Friday) March 2, 9, 
23, 30, April (no class April 6) 13, 20. Depending on my out of state travel, 
some of these dates may have to be altered.  We will probably add another 
Thursday on at April 27 if needed.

This is the first time I have taught a class in the electronic classroom.  There 
may be some bugs that need to be worked out.  Please bring a floppy disk so you 
can take some data back with you.  

The first class will deal with assembling complete protein sequences from ESTs.

D. Nelson

Course members Biochem 920 Bioinformatics

Bothner, Brian
Yuan, Gao
Kendall, Ryan
Kulkarni, Ajit
Kumaraswami, Muthiah
Ma, Ji
Menon, Swapna
Mo, Yongkai
Moon, Sun Young
Moxley, Robert
Shen, Ying
Sickmier Ernest
Tao, Jianning


Andhare, Roopa
Howe, Martha
Hori, Rod
Zheng, Yi

Bookmarks for Bioinformatics
First problem
Second problem
Sequences for Feb. 3 class

Feb. 3 class summary and comments

Feb. 10 class summary and comments

Feb. 17 class summary and comments

Feb. 25 class summary and assignment

March 9 class summary and comments

March 9 class assignment 4

A database of 33 mitochondrial carriers from C. elegans
For use in the Feb. 10 class.

44 assembled mitochondrial carriers from Drosophila

A partial table of highly abundant ESTs in UNIGENE
Please go to the shared folder and read the file called seq55.genomic.
I placed this there on Monday Feb 7 to show how to assemble a gene from 
genomic DNA.
Drosophila accession numbers for carriers an alphabetical list of mito carriers 
for the Feb. 10 class.
Blast search list for in class searches Feb. 10 class
Blast search list for in class searches Feb. 17 class
Clustal W server for Feb. 25th class
An alignment of 32 yeast carriers Feb. 25th class
Prosite in Switzerland
Pfam database in St. Louis
Blocks at Fred Hutchinson Cancer Research 
Center, Seattle

HSP-90 beta N-terminal

To find a polymorphism in genbank do a TBLASTN search of this sequence against the human EST section of Genbank.

Links to Clustal W and Phylip for use on the web provided by Brian Bothner
SDSC workbench
Pharm207 course

Human P450s
Expasy Expert Protein Analysis System
CYP27C1 data