Workshop: Introduction to Bioinformatics

The sequencing and deep resequencing of complete genomes, microarray platforms and other high throughput technologies has generated an unprecedented deluge of data that needs to be stored, analyzed, annotated, classified, parsed and deciphered. Bioinformatics is playing a crucial role in the search, analysis, and the storage of such sequence and biological data. Bioinformatics addresses issues related to the storage, retrieval and analysis of information about these biological data from assembly of sequence fragments, analysis of DNA, RNA and protein sequences, their structure and function, to prediction of gene locations and genome annotation. After a general introduction to molecular biology, the workshop gives an overview of bioinformatics and computational biology. Topics that will be addressed include the analysis of DNA and protein sequences, databases creation and search, phylogenetics, genetic linkage and association including genome-wide association studies, RNA secondary structure prediction, gene prediction, and gene expression microarrays.

The workshop consists of lectures, demonstrations, tutorials and hands-on sessions. The hands-on exercises use online publicly available tools and will enhance the understanding of common bioinformatics tasks. The workshop does not assume deep knowledge in molecular biology and no strong computer skills are needed. In other words, no prior knowledge of biology is needed but an interest in molecular biology and genetics is essential. Although this workshop is primarily designed to provide information for researchers, educators and students as a practical introduction to Bioinformatics, experienced fellows can also find this course to be useful.

Copy of lecture notes, hands-on exercises and case studies for all sessions, from Monday, January 7 to Saturday, January 12, 2013

Cover Sheet

Lecture Notes Biology Motivation Algorithm Hands-On Exercise Additional Links Articles
Biology Review
What is Bioinformatics?
Transcription and Translation Transcription Translation Algorithms ONE: Human Traits
TWO: Interesting Problems
Biology Terms
Interactive Exercise
A Sunny Day (video 6.1 MB)
Transcription (video 1.6 MB)
Translation (video 2.0 MB)
Translation (YouTube)
Biologie (in French)
Bioinformatique (in French)
Luscombe et al.
Pairwise Sequence Alignment
Pairwise Sequence Alignment DP for Alignment Algorithm THREE: Investigating Inherited Diseases
DP for Alignment Problems (visualization in Java)
Needleman et al.
Multiple Sequence Alignment
Multiple Sequence Alignment CLUSTAL Algorithm FOUR: Multiple Sequence Alignment CLUSTALW Higgins
Phylogenetic Trees
Phylogenetic Tree Construction UPGMA Algorithm Biology Workbench
FIVE: Phylogenetic Tree
UPGMA: An Example Baldauf
RNA Structure Prediction RNA Secondary Structure Prediction Nussinov Algorithm SIX: RNA Secondary Structure Predicition
Sequences for RNA
DP for RNA Prediction Problem Eddy
Gene Prediction Gene Prediction VEIL algorithm SEVEN: Gene Prediction
List of known Arabidopsis Splice Sites
VEIL Brent et al.
Human Genome Variation Human Genome Variation Microarray Design EIGHT: Human Genome Variation GWAS Pearson
The Big Jaw The Big Jaw Case Study NINE: The Big Jaw
Supplementary Info Stedman et al.
Beta Thalassemia Beta Thalassemia Case Study TEN: Beta Thalassemia
Treisman et al.
Videos on Thalassemia
Agouti et al.
Lemsaddek et al.
HIV HIV Case Study ELEVEN: HIV Genome
Genome Maps of 3 HIVs
TWELVE: The Origin of HIV
The Nine Genes of HIV Rambaut et al.
Structural Bioinformatics
by Natalia Khuri
Structural Bioinformatics . THIRTEEN: Protein Secondary Structure
FOURTEEN: Protein Structure Visualization
FIFTEEN: Molecular Modeling
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Bits and Pieces Bits and Pieces . . . .

Acknowledgement: I would like to thank Natalia Khuri for her help in preparing the workshop, David Matthes and Chris Brinegar for letting me sit in their biology classes, and Robert Fowler for letting me audit and participate in 3 genetics classes.

Sami Khuri, Professor
Department of Computer Science
San José State University
One Washington Square
San José, CA 95192-0249
Tel. (408) 924-5081
Fax (408) 924-5062

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