CSC 691: Bioinformatics (Introduction to bioinformatics algorithms)

Course Description

Bioinformatics is a rapidly evolving field that studies biological systems and biological data (such as DNA/protein sequences, macromolecular structures and functional genomics data) using analytic theory and practical tools of computer science, mathematics and statistics. The topics include concepts of molecular genetics, biological databases, database searching, sequence alignments, phylogenetic trees, structure prediction, and microarray data analysis.

Textbook

Introduction to Bioinformatics 4e. Arthur M. Lesk.  http://global.oup.com/uk/orc/xedition/leskbioinf4exe/

Course Schedule   (Tentative schedule, slides will be uploaded, more topics will be added)

• Chapter 1: Introduction
• Chapter 2: Genome organization and evolution
• Chapter 4: Archives and information retrieval
• Chapter 5: Alignments and phylogenetic trees   
• Computational Analysis of Metagenomes

Project  Assembling ORFs from metagenomic sequences

Task 1:  Data acquisition (Due March 21st, in clas presentation)

• Find a metagenomic project of your choice. It is better to find project that has annotation information in order to help in your testing later.
• Download the data and read in the files (fasta or fastq). You may use your prefered language. Note that there are libraries and toolboxes for Bioinformatics for most major scripting and compiled languages.

Task 2:  ORF extraction. (Due April 4th)

• Using ORFExtractor or by implementing your own ORF extractor: Write a program to extract complete and incomplete ORFs from the metagenomic reads in your project.
• If you use ORFExtractor, you would need to modify the code to save complete and incomplete ORFs seperately.

Taks 3:  Assembling the ORFs

• Read the following two papers: ( We will discuss them in class)
  • AN ORFOME ASSEMBLY APPROACH TO METAGENOMICS SEQUENCES ANALYSIS:
    • http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2829862/
  • SPA: a short peptide assembler for metagenomic data: 
    • http://www.ncbi.nlm.nih.gov/pubmed/23435317
•  

Task 4:  Testing and comparison

Task 5: Documnetiaon