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
Introduction

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 myDNA 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 HandsOn_Sequences.txt	DP for Alignment Problems DP.zip (visualization in Java) instructions	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 arabidopsis_rad1_genomic.html arabidopsis_rad1_cDNA.html 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 myh16_Sequences.txt	Supplementary Info	Stedman et al.
Beta Thalassemia	Beta Thalassemia	Case Study	TEN: Beta Thalassemia beta_globin_sequence	Treisman et al. Videos on Thalassemia	Agouti et al. Lemsaddek et al.
HIV	HIV	Case Study	ELEVEN: HIV Genome hiv_sequence.txt Genome Maps of 3 HIVs TWELVE: The Origin of HIV env_protein_sequences.txt gag_protein_sequences.txt pol_protein_sequences.txt	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	.	.
BRCA1	BRCA1	Case Study	SIXTEEN: BRCA1 Gene sequences_BRCA1.txt	.	.
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
E-mail: khuri@cs.sjsu.edu

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