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Kingsborough Community College of The City University of New York
Department of Biological Sciences

Biology 60/CIS 60: Computer Applications in Bioinformatics

Bulletin Description

This course demonstrates the applications of computers in Bioinformatics. From an introduction to biochemistry topics proceed to Genomics and computer-related applications. Analyses of the genetic sequences and their corresponding three dimensional structures will be done. Examples are given of how computers are used to do sequence searches and sequence comparisons (homologies). The algorithms used to perform searches and comparisons are provided. Computers are used to do gene analyses in the area of DNA, protein, and RNA prediction of sequences and structures. The course includes a computer laboratory and a wet laboratory in Genomics.

Topical Course Outline

Lesson /Lab
Every lecture and every laboratory are a two hour session
M= Math Faculty B= Biology Faculty

Week 1. General Introduction to Computer Technology-Algorithms 1-M 1-M
Lab 1: Euclid’s Algorithm to find Greatest Common Divisor as a
background to understanding computer modeling.

Week 2. Introduction to Genomics 2-B 2-B
Lab 2: Finding a gene in a DNA sequence

Week 3. Searching Data Bases 3-M 3-B
a. PubMed /Medline
b. Retrieving Protein Sequences
c. Retrieving DNA Sequences
Lab 3: Comparing a given sequence across species (cytochrome
oxidase genes in fungi, plants, and animals)

Week 4. Working with Nucleotide Sequence Databases-I 4-B 4-B

  1. Analyzing DNA Composition-(C-G Content,

Counting Words in DNA, Finding Repeats)
b. Simple genes
c. Complex genes
d. Using GenBank
e. Finding Protein Coding Regions
f. Assembling Sequence Fragments
g. Genome Databases

  1. Human Genome

Lab 4: Restriction enzyme analysis of DNA sequence
(Digestion of lambda-DNA)

Week 5. Working with Nucleotide Sequence Databases-II 5-M 5-M

a. Sequence Homology-BLAST
b. Gene Prediction Methods & Algorithms
c. Hidden Markov Models
d. Gene Prediction Programs
e Visualization and Integration Tools
Lab 5: FOXP2 gene is used to illustrate gene prediction

Week 6. Working with RNA 6-B 6-M
a. RNA Secondary Structure Thermodynamics
b. Dynamic Programming

  1. Programs Available for RNA Secondary Structure

d. Interactively Drawing RNA Secondary Structures
e. Predicting RNA Tertiary Structure
f. Searching Databases and Genomes for RNA Sequences
Lab 6: Prediction of secondary structure and sequence alignment
for two sequences

Week 7. Working with a Single Protein Sequence-I 7-B 7-B
a. Biochemistry on a Computer
b. Primary Structure Analysis
c. Predicting Methods Using Protein Sequences
Lab 7: (Wet Lab) Protein purification (green florescent
protein from bacteria)

Week 8. Working with a Single Protein Sequence-II 8-M 8-M
a. Sequence Homology-BLAST
b. Neural Networks
c. Predicting Post-Translational Modifications in a Protein
d. Finding Domains in a Protein
Lab8: Gene Analysis of the protein Rhodopsin

Week 9. Comparing Two Sequences 9-B 9-M
a. Choosing the Right Sequence
b. Dot Plot
c. Making Local Alignments over the Internet
d. Making Global Alignments over the Internet
e. Dynamic Programming Algorithm
Lab 9: Identifying human genes within a given sequence.
Identifying orthologous regions in other organisms

Week 10. Working with Protein 3-D Structure 10-B 10-M
a. Primary-Secondary Structures
b. 3-D Structure- PDB (Protein Data Bank)
c. Protein Classification
d. Alignment of Protein Structures
e. Dynamic Programming
f. Structural Prediction
g. Homology Modeling
h. Folding Proteins in a Computer
i. Threading Sequences onto PDB Structures
Lab 10: Finding different structures of the protein calmodulin

Week 11. Intermolecular Interactions & Biological Pathways 11-B 11-M
a. Pathway & Molecular Interaction Databases
b. Prediction Algorithms for Pathways & Interactions
c. Resources for Interaction Prediction
d. Network & Pathway Visualization Tools
Lab 11: Using the given sequence of the yeast tryptophan
biosynthesis enzyme, its function and possible
biomolecular interactions are predicted

Week 12. Applications 12-B 12-B
Molecular Medicine, Personalized Medicine, Preventative
Medicine, Gene Therapy, Drug Development, Biotechnology
Forensic Analysis
Lab 12: (Web Lab) Forensic Analysis (crime scene sample analysis)

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