Introduction to Bioinformatics BI420 – Introduction to Bioinformatics Introduction to Bioinformatics BI420 2012 Fall Semester Boston College

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

BI420 – Material Introduction to Computational Genomics: Cristianini and Hahn Additional materials: www.computational-genomics.net

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

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

BI420 – Software MATLAB http://www.bc.edu/software/applications/research/matlab.html 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

Genomes and Genes

The animal cell

DNA – the carrier of the genetic code

DNA organization – chromosomes

DNA organization – mitochondria

Translation of genetic information

Gene organization

Protein structure

RNA structure

Gene prediction, genome annotation

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

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

Gene expression Expression profiling technologies and analysis approaches

Classical Bioinformatics Methods

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

Biologically significant alignment

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.)

The Tree of Life

Evolution of chromosome organization

Phylogenetics How can evolutionary relationships be reconstructed?

Population and Personal Genomics

Population genetics

Medical Genomics Medical applications of sequencing individuals

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

Practical Bioinformatics

MATLAB Performing bioinformatic analysis using MATLAB

UNIX scripting Using a command-line operating system

PERL programming Programming in PERL within a UNIX OS

Managing a Database CLONE id name received masked 1 NH0260K08 12-25-99 12-26-99 2 NH0407F02 12-28-99 01-03-00 HIT id cloneID hspID start end 1 1 1 1 17957 2 2 1 96912 114891 ALLELE id hitID nucleotide 1 1 C 2 2 T mySQL. Accessing bioinformatics databases, processing data, and building webpages from PERL.