Workshop in Bioinformatics 2010 Class # Class 8 March 2010

(Molecular) Bioinformatics  Development (Computational Biology)  New algorithms and statistics to assess biological information  Tools for access and management different types of information (DB, Models, Maps..)  User view (applied Bioinformatics)  Analysis: interpretation of various types of data (nt, aa, domains, RNAs, signatures, 3D-structures)  Statistical methods  Applying predictions methods (from the shelf)  Applying tools (web, programs…)

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

What do you mean “raw data”… Raw (primary) Data Sequences RNA (many types) DNA Genome Variations SNP Mutations Copy Number Variations (CNV)

What do you mean “raw data”… Rate - Raw (primary) Data HM1: Identify 2 areas with a similar (?) trend

The level of resolution: the ‘basic unit’ example DNA Nucleotide to Genome level NOTE: Not always the technology identify nucleotide in the DNA HW2: provide an example…list the technology

The level of resolution: the ‘basic unit’ example DNA Nucleotide to Genome level Technology: DNA / RNA SEQUENCING Nucleotide level

DNA Sequencing “Classical” (Sanger)

The level of resolution: the ‘basic unit’ example DNA TECNOLOGY definitions: Nucleotide (1) Run ( ) ABI –Sanger fluorescence capillary Reads (35-400) SOLEXA and 454 (WGS) – BUT millions in parallel

ABI x700 bases Scale: capillary tech RUNs New technology “454” technology (not in this class)

The level of resolution: the ‘basic unit’ example DNA FUNCTIONAL / Assembly definition (more)  SNP (1)  Indel (1-1000s) human genome -average 5 bp  EST ( )  Gene (1000 bacteria; 100,000 human; huge range)  Contig- 500,000, huge range / BacTig >10 6  Chromosome: Bacteria: 4*10 6, Human: *10 6  Genome: HUGE ranges from virus 5*10 3 to frog 5*10 10

Shotgun Sequencing

“classical” Sequencing

Deep Sequencing New fast and cheap methods for sequencing Replacing ? ‘classical’ Sanger sequencing (covered if time allows…)

The level of resolution: the ‘basic unit’ example DNA Is genome is the “largest unit” ? 2008: MetaGenomics The BIOME project : A community of genomes in human body

SEARCH for numbers… How many nucleotides in chromosome 7 of human…. 1.Search “Google like” 2.Search “PubMED like” 3. Your way HM3: the value, the source

The SOLUTION Dedicated resources (=Databases) that are focused for the genome ‘building blocks’ 1.NCBI 2.EBI 3. more… Centralized Achieve for DB, Tools, Protocols, Books, Drugs, education etc