Curriculum 2005

 

Lecture Title Date & Time html .ppt Workshop References
Program Overview Mon 6/13
9:00-12:00pm		 view download    
Molecular life Science Review Mon 6/13
1:00-2:30pm		 view download workshop  
Python I Mon 6/13
2:30-4:00pm		 view download workshop reference
Literature Databases Tues 6/14
9:00-12:00pm		 view download workshop reference
Sequence Comparisons Tues 6/14
1:00-4:00pm		 view download workshop reference
Python - II Wed 6/15
9:00-12:00pm		 view download    
Python - III Wed 6/15
1:00-4:00pm		 view download    
Database Searching Tues 6/16
9:00-12:00pm		 view download workshop reference
Global and Local Alignment Thurs 6/16
1:00-4:00pm		 view download   reference
Professional Development Fri 6/17
9:00-12:00pm		        
Research Site Visit Fri 6/17
1:00-4:00pm		        
Statistics I Mon 6/20
9:00-12:00pm		   PDF    
Statistics II Mon 6/20
1:00-4:00pm		   PDF    
Statistics III Tues 6/21
9:00-12:00pm		   PDF    
Sequence Databases Tues 6/21
1:00-4:00pm		 view download workshop reference
Rationale for Searching Seq DB Wed 6/22
9:00-12:00pm		 view download   reference
Longest Common Substring Algorithm (LCS) Wed 6/22
1:00-4:00pm		 view download    
Python IV Thurs 6/23
9:00-12:00pm		 view download    
Local and Global Alignment Thurs 6/23
1:00-4:00pm		 view download    
Space Efficient Alignment Algorithms Fri 6/24
9:00-12:00pm		 view download    
Research Seminar Fri 6/24
1:00-2:00pm		        
Multiple Sequence Alignment Mon 6/27
9:00-12:00pm		 view download workshop reference
Protein Structure Prediction Mon 6/27
1:00-4:00pm		 view download   reference
Ethics of the Human Genome Tues 6/28
9:00-12:00pm		        
Phylogenetics Tues 6/28
1:00-4:00pm		     workshop  
Protein Structure Wed 6/29
9:00-12:00pm		 view download workshop reference
Proteomics -2D Gel Tlectrophoresis Wed 6/29
1:00-4:00pm		 view download workshop reference
Programming Workshop Thurs 6/30
9:00-12:00pm		        
Signal Transduction Pathways Thurs 6/30
1:00-4:00pm		 view download    
First Year Students Demonstrate Local Alignment Project Fri 7/1
9:00-12:00pm		        
Beach Party Fri 7/1
9:00-12:00pm		        
Microarrays-Cluster Analysis I Tues 7/5
1:00-4:00pm		 view download    
Work at Research Site Tues 7/5
1:00-4:00pm		        
Microarrays-Cluster Analysis II Wed 7/6
9:00-12:00pm		 view download    
Work at Research Site Tues 7/6
9:00-12:00pm		        
Microarrays-Cluster Analysis III Thurs 7/7
1:00-4:00pm		 view download    
Work at Research Site Thurs 7/7
1:00-4:00pm		        
First Year Students Present Written Assignments Fri 7/8
9:00-12:00pm		        
Evaluation of Didactic Faculty,
Work at Research Site		 Frii 7/8
1:00-4:00pm		        

Workshop

Workshop #2

Workshop A: Set up a cubby account on a biological topic of interest. Show the instructor the cubby account you set up. Subscribe to NCBI News.

Workshop B: Go to OMIM Website and type "Breast cancer". Link to MIM#113705. What does the light bulb represent? What do the links with the numbers lead to? Obtain the following information on BRCA1: Chromosome location -- Method used to map the BRCA1 gene to that particular location in the chromosome. Name the disease gene that is telomeric and the disease gene that is centromeric to BRCA1.
Obtain protein sequence and cDNA sequence.

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Workshop #3

Consider the sequence GAACTCATACGAATTCACGTCAGCCCATCG

Use a window of 3 nucleotides and slide the window 1 nucleotide at a time. Calculate the %GC as a function of nucleotide number. Draw a graph. Change the window to 2 nucleotides. Then overlap the two plots. You may use Excel. Print out the spread sheet and the graph.

Find the protein sequence for bacteriorhodopsin. Make sure you obtain the full-length sequence. Find the Kyte-Doolittle Hydropathy program software at the Expasy Tools website. Perform Kyte-Doolittle Hydropathy analysis of bacteriorhodopsin. Compare the plot to the one displayed in lecture today. Are there differences in the two plots? If so, why?

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Workshop #4

A. Download PAM250 and PAM10 from internet and print out. What are the differences between the two matrices? Why do you see these differences?

B. Download BLOSUM67 and BLOSUM30. What are the differences between the two matrices? Why do you see these differences? Download the BLOSUM30 matrix as a text file onto the C drive and name. Name the file BLOSUM30.

C. Import the human p53 (Accession number AAH03596) and squid p53 (Accession number AAA98563) sequences from the protein databases at NCBI onto your hard drive in FASTA format. This can be accomplished by changing the display format on the ENTREZ screen to FASTA. Then highlight the entry and copy onto clipboard. Then open NotePad on your local hard drive. Paste each sequence into a separate document and save them in a folder named sequence on C drive. Name the documents p53_human and p53_squid. Then type dotter c:\sequence\p53_human.txt c:\sequence\p53_human.txt RETURN. Do you detect some parallel lines? Why? What does the greyramp tool do? Capture the image and save..

D. Type dotter c:\sequence\p53_human.txt c:\sequence\p53_squid.txt RETURN. What is the difference between the human vs. human comparison and the human vs. squid comparison?

E. Change the matrix from BLOSUM67 to BLOSUM30 by typing in the following command: dotter -M c:BLOSUM30.txt a:\sequence\p53_human.txt c:\sequence\p53_squid.txt. Which scoring matrix produces more lines? Why?

F. If you have time, obtain the mouse p53 sequence and compare to human. According to your analysis, do you detect more similarity with human or squid. Are some subregions within the p53 protein more conserved than others?

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Workshop #5

1. Use your knowledge of dyanamic programming to find the optimal alignments between AATGC and AGGC. Using the Payoff matrix discussed in the lecture what is the score for the optimal path?

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Workshop #6

Write a Python program to compute the hydrophobicity of an amino acid. Program will prompt the user for an amino acid and will display the hydrophobicity

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Workshop #7

Write a sliding window program to compute the %GC in a sequence of nucleotides. The program should prompt the user for 1) The DNA sequence. 2) The window size (assume the window increment is 1). Test your program using the data for Workshop 3.

** Demonstrate your solution at the beginning of class on May 3rd. Time will be spent at beginning of class on debugging solutions to get them working properly.

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Workshop #9

1) Use the following accession number to find a sequence in a nucleotide database: Z68198.

2) Print out the first 1000 nucleotides of the cosmid and decifer the open reading frames from the annotations listed in the flat file.

3) Underline the open reading frames and give direction of the coding strand (5' to 3').

4) Show to the instructor.

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Workshop #10

Go to NCBI Website. Open BLAST Website. Perform BLASTP on the sequence SSSVPSQKTYQGSYGFRLGFLHSGTAKSVT. Use default settings. Record the total number of letters in the NR database and the E-value for the top hit. Next, change the database to SwissProt and repeat. Record the total number of letters in the Swiss-Prot data base and the E-value for the top hit. Compare the E-values for the two searches and explain why they are different. Do you think that you obtained these hits by chance? Attempt to find another database so that the search would give you hit with even a lower E-value? What other parameters can you change to give you a score with a lower E-value?

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Workshop #15

Use Entrez to find the C-terminal region (approximately 215 residues) of human BRCA1 (SWISS-PROT accession number P38398). Search the NR protein database with this sequence using PSI-BLAST. Why do some new scores have lower E values than the old scores after the second iteration?

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Workshop #17

Workshop A: Find the complete amino acid sequence of human p53 and perform a secondary structure prediction with PSIPRED or another secondary structure prediction algorithm. Have the results emailed to you.

Workshop B: Check to see if the BLIMPs program in the BLOCK searcher can predict the function of PTEN (NP_000305). PTEN is an abbreviation for phosphatase and tensin homolog Obtain sequence from protein database at NCBI. Convert to FASTA format. Paste sequence into window in BLOCK Searcher ( http://blocks.fhcrc.org/blocks/blocks_search.html). Determine the major function based on thee BLOCK Searcher output. Determine the actual function of PTEN by performing a text search for PTEN in the OMIM database. Did this BLOCK searcher help assess the function of PTEN?

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Workshop #18

Download structure coordinates for 1HEW protein from PDB onto your hard drive. Follow the tutorial for viewing protein structures at http://www.usm.maine.edu/~rhodes/SPVTut/text/SPdbVTut.html. You can start the tutorial at Section 2--Windows and help.

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References

References for Lecture #1

Gelehrter, Collins, Ginsburg, Principles of Medical Genetics, Williams & Wilkins, Baltimore, 1998.
Baxevanis and Ouellette, Bioinformatics-2nd Edition, Wiley-Interscience, New York, 2001
http://cmgm.stanford.edu/classes/csuh/

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References for Lecture #2

http://adonis.creighton.edu/hsl/Searching/Medline-Fields.html
http://cmgm.stanford.edu/classes/csuh/literature/
http://hml.org/WWW/class/help/medcite.html
http://www.nlm.nih.gov/mesh/meshhome.html

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References for Lecture #3

Baxevanis and Ouellette, Bioinformatics, Wiley-Interscience, New York, 2001
http://www.infobiogen.fr/doc/dotter.html
http://info.bio.cmu.edu/Courses/BiochemMols/BCMolecules.html

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References for Lecture #4

http://www.techfak.uni-bielefeld.de/bcd/Curric/PrwAli/nodeD.html#2page6
Baxevanis and Ouellette, Bioinformatics, Wiley-Interscience, New York, 1998
http://cmgm.stanford.edu/classes/csuh/literature/
http://www.infobiogen.fr/doc/dotter.html

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References for Lecture #5

http://www.finchcms.edu/biochem/Walters/nw.html
Baxevanis and Ouellette, Bioinformatics, Wiley-Interscience, New York, 1998
http://cmgm.stanford.edu/classes/csuh/search1/
http://bioweb.pasteur.fr/docs/doc-gensoft/EMBOSS/doc/programs/text/needle.txt
http://www.maths.tcd.ie/~lily/pres2/sld003.htm
http://www.sbc.su.se/~per/molbioinfo2001/dynprog/dynamic.html

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References for Lecture #9

http://www.ncbi.nlm.nih.gov/Sitemap/index.html#GenBank
Baxevanis and Ouellette, Bioinformatics 2nd Ed, Wiley-Interscience, New York, 2001
Misener and Krawetz, Bioinformatics Methods and Protocols, Humana Press, Totowa, NJ, 2000

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References for Lecture #10

Baxevanis and Ouellette, Bioinformatics, Wiley-Interscience, New York, 1998
http://www.ncbi.nlm.nih.gov/BLAST/blast_FAQs.html#Expect
http://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html
http://www.calstatela.edu/faculty/jmomand/FacultyWorkshop_01/ProbabilityMethods_files/v3_document.htm
http://www.wikipedia.org/wiki/Bayes%27_theorem

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References for Lecture #11

http://www.math.tau.ac.il/~rshamir/algmb/scribe00/html/lec03/lec03.html
Baxevanis and Ouellette, Bioinformatics, Wiley-Interscience, New York, 1998
http://cmgm.stanford.edu/classes/csuh/literature/
Misener, S. and Krawetz, Bioinfomatics Methods and Protocols, Humana Press, Totowa, 2000
http://searchlauncher.bcm.tmc.edu:9331/help/AlignmentScore.html
http://barton.ebi.ac.uk/papers/rev93_1/subsection3_7_6.html
http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/Seg.html

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References for Lecture #12

http://www.sbc.su.se/~per/molbioinfo2001/dynprog/dynamic.html
Lectures: Database search (4/16) and Rationale for DB Searching (5/16)
Computational Molecular Biology – An Algorithmic Approach, Pavel Pevzner
Introduction to Computational Biology – Maps, sequences, and genomes, Michael Waterman
Algorithms on Strings, Trees, and Sequences – Computer Science and Computational Biology, Dan Gusfield
http://www.sbc.su.se/~arne/kurser/swell/pairwise_alignments.html

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References for Lecture #15

Misener and Krawetz (Eds), Bioinformatics, Methods and Protocols, vol. 132, Humana Press, Totowa, 2000 pp 185-219
Baxevanis and Ouellette, Bioinformatics 2nd ed. , Wiley-Interscience, New York, 2001
http://www.dkfz-heidelberg.de/tbi/bioinfo/Variants/LocalAli/
http://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/BLAST/slide_list.html

References for Lecture #17

Pietrokovski et al., The Blocks Database-A system for protein classification.
Baxevanis and Ouellette, Bioinformatics 2nd edition, Wiley-Interscience, New York, 2001
http://www.sbc.su.se/~arne/kurser/swell/secstrpred.html
http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10493868&dopt=Abstract
http://www.chembio.uoguelph.ca/educmat/chm730/f730.html

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References for Lecture #18

http://www.usm.maine.edu/~rhodes/SPVTut/text/SPdbVTut.html
http://www.sbc.su.se/~arne/kurser/swell/secstrpred.html
http://www.expasy.ch/swissmod/course/text/chapter6.htm
http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml

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References for Lecture #19

http://swissmodel.expasy.org//course/text/chapter6.htm
Wang et al., Nucleic Acids Research 28, 243-245, 2000.
http://www.iucr.org/iucr-top/comm/ccom/School96/pdf/sb.pdf

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