Workshop in Bioinformatics 2009 Class 2 Michal Linial Room A-515

Workshop in Bioinformatics (2) Bioinformatics is the computer-assisted data management discipline : Gather, store, analyze, integrate biological and genetic information (data), and represent this information efficiently.

Workshop in Bioinformatics (3) Principle: Biology, computer science, and information technology merge into a single discipline Big Goal: Discovery of new biological insights. Create a global perspective of living system Formulate unifying principles in biology From ‘unknown’ to ‘known’ Fast, efficient way to extract information

Bioinformatics - two faces  Analysis and interpretation of various types of data (sequences nt, aa, domains, signatures, structures, RNAs)  Development of new algorithms / statistics to assess biological information  Development and implementation of tools for access and management different types of information (DB, Models, Maps..)

What do you mean by “data”… Raw (primary) Processed (analyzed) Integrated (systems)

What do you mean by “data”… Raw (primary) Data Sequences RNA DNA Genome Variations SNP Mutations

DNA Sequencing 5’ 5’ Primer 3’ Template G C A T G C dATP dCTP dGTP dTTP ddATP dATP dCTP dGTP dTTP ddCTP dATP dCTP dGTP dTTP ddTTP dATP dCTP dGTP dTTP ddGTP GddC GCATGddC GCddAGCAddTddG GCATddG “Classical” (Sanger)

ABI x700 bases G C T A + _ + _ GCATGCGCATGC short long capillary unit New technology “454” technology (not in this class)

What do you mean data… Raw (primary) Data Sequences RNA DNA Genome Variations SNP Mutations

Shotgun Sequencing Isolate Chromosome ShearDNA into Fragments Clone into Seq. Vectors Sequence

Shotgun Sequencing Sequence Chromatogram Send to Computer Assembled Sequence

Rat Sequencing

Deep Sequencing New fast and cheap methods for sequencing Replacing ? ‘classical’ Sanger sequencing (not covered in this class but introduced later)

The main topics Introduction to databases Working with sequences / Pairwise comparison Database similarity searching Profile building and searching Functional resources Genomics Proteomics Integrative resources Introduction to systems biology More…

The goal of the course  Introduction to variety of databases and tools  Independence in working with available resources  Critical evaluation of web tools  Exposure to the main needs of modern biologist  Leverage your research skills  Discussing key issues in “new biology”  Presenting front-line research projects based on BI ….but mainly fun