1. Introduction to Bioinformatics
BI420 – Introduction to Bioinformatics
Introduction to Bioinformatics
BI Fall Semester
Boston College

2. BI420 – Course information
Instructor: Prof. Gabor Marth
Teaching assistant: Jiantao Wu
Wiki site with updated syllabus and powerpoints:
This will be updated regularly and will supersede printed syllabus. You are expected to keep up with any changes made there.

3. BI420 – Material Introduction to Computational Genomics:
Cristianini and Hahn
Additional materials:

4. BI420 – Material (cont’d) Recommended books
Primary literature, both mandatory and optional (see Syllabus)
Reference materials (for Practical Bioinformatics)
Lecture PPTs will be online

5. BI420 – Grading Homework (4): 40% Midterm exams (3): 45%
In-class presence & participation: 15%

6. BI420 – Software
MATLAB
Install this and view the “demo” by next class. To do this type “demo” at the MATLAB command line.
UNIX/PERL
We will introduce these when we get to the Practical Bioinformatics section

7. Genomes and Genes

8. The animal cell

9. DNA – the carrier of the genetic code

10. DNA organization – chromosomes

11. DNA organization – mitochondria

12. Translation of genetic information

13. Gene organization

14. Protein structure

15. RNA structure

16. Gene prediction, genome annotation

17. The informatics of DNA sequencing
Steps in the production and analysis of sequencing data

18. Genetic variation discovery & analysis
look at multiple sequences from the same genome region
use base quality values to decide if mismatches are true polymorphisms or sequencing errors

19. Gene expression
Expression profiling technologies and analysis approaches

20. Classical Bioinformatics Methods

21. Sequence alignment and similarity search
Given a sequence, how can one tell which species it comes from? How can one identify evolutionarily related sequences?

22. Biologically significant alignment

23. Storage/retrieval of biological data
August 2010
Genbank whole-genome sequences:
169 billion bp
Genbank other sequences:
117 billion bp
Gene expression omnibus:
480,000 samples (microarray, RNA-seq, ChIP-chip, ChIP-seq, RIP-seq, etc.)

24. The Tree of Life

25. Evolution of chromosome organization

26. Phylogenetics
How can evolutionary relationships be reconstructed?

27. Population and Personal Genomics

28. Population genetics

29. Medical Genomics
Medical applications of sequencing individuals

30. Personal genome sequencing
How soon will everyone be sequenced? Ethical issues.

31. Practical Bioinformatics

32. MATLAB
Performing bioinformatic analysis using MATLAB

33. UNIX scripting
Using a command-line operating system

34. PERL programming
Programming in PERL within a UNIX OS

35. Managing a Database
CLONE
id name received masked
1 NH0260K
2 NH0407F
HIT
id cloneID hspID start end
ALLELE
id hitID nucleotide
1 1 C
2 2 T
mySQL. Accessing bioinformatics databases, processing data, and building webpages from PERL.