Bioinformatics Antal, Péter Hullám, Gábor Millinghoffer, András Hajós, Gergely Marx, Péter Arany, Ádám Bolgár, Bence Gézsi, András Sárközy, Péter Poppe, László Created by XMLmind XSL-FO Converter. Bioinformatics írta Antal, Péter, Hullám, Gábor, Millinghoffer, András, Hajós, Gergely, Marx, Péter, Arany, Ádám, Bolgár, Bence, Gézsi, András, Sárközy, Péter, és Poppe, László Publication date 2014 Szerzői jog © 2014 Antal Péter, Hullám Gábor, Millinghoffer András, Hajós Gergely, Marx Péter, Arany Ádám, Bolgár Bence, Gézsi András, Sárközy Péter, Poppe László Created by XMLmind XSL-FO Converter. Tartalom Bioinformatics .................................................................................................................................... 1 1. 1 DNA recombinant measurement technology, noise and error models ............................... 1 1.1. 1.1 Historic overview ............................................................................................... 1 1.1.1. 1.1.1 Clinical aspects of genome sequencing ............................................... 2 1.1.2. 1.1.2 Partial Genetic Association Studies .................................................... 2 1.1.3. 1.1.3 Genome Wide Association Studies ..................................................... 2 1.2. 1.2 First generation automated Sanger sequencing ................................................... 2 1.3. 1.3 Next generation sequencing technologies ........................................................... 3 1.3.1. 1.3.1 Pyrosequencing and pH based sequencing .......................................... 4 1.3.2. 1.3.2 Reversible terminator based sequencing ............................................. 5 1.3.3. 1.3.3 Nanopore based sequencing ................................................................ 6 1.4. 1.4 Error characteristics of Next Generation Sequencing ......................................... 7 1.4.1. 1.4.1 Carry forward/incomplete extension ................................................... 7 1.4.2. 1.4.2 Homopolymer errors ........................................................................... 8 1.5. 1.5 Capture technologies .......................................................................................... 8 1.5.1. 1.5.1 PCR capture ........................................................................................ 8 1.6. 1.6 Emulsion PCR .................................................................................................. 11 1.7. 1.7 Bridge amplification ......................................................................................... 11 1.8. 1.8 Targeted resequencing ...................................................................................... 12 1.9. 1.9 De-novo sequencing ......................................................................................... 12 1.10. 1.10 Next generation sequencing workflows ........................................................ 12 1.10.1. 1.10.1 Filtering ......................................................................................... 13 1.10.2. 1.10.2 Mapping ........................................................................................ 13 1.10.3. 1.10.3 Assembly ....................................................................................... 13 1.10.4. 1.10.4 Variant calling ............................................................................... 13 1.10.5. 1.10.5 Paired end sequencing ................................................................... 13 1.11. 1.11 Multiplexing samples .................................................................................... 14 2. 2 The post-processing, haplotype reconstruction, and imputation of genetic measurements 14 2.1. 2.1 Genome ............................................................................................................. 15 2.2. 2.2 Genotype ........................................................................................................... 15 2.2.1. 2.2.1 Single nucleotide polymorphisms ..................................................... 15 2.2.2. 2.2.2 Types of point mutation .................................................................... 16 2.3. 2.3 Haplotypes and recombination ......................................................................... 16 2.4. 2.4 Linkage Disequilibrium .................................................................................... 16 2.5. 2.5 Haplotype reconstruction .................................................................................. 18 2.6. 2.6 Imputation ......................................................................................................... 19 2.7. 2.7 Genotyping platforms ....................................................................................... 19 2.7.1. 2.7.1 Sample preparation ............................................................................ 20 2.7.2. 2.7.2 Regions of interest ............................................................................. 20 2.7.3. 2.7.3 Primer Design .................................................................................... 20 2.7.4. 2.7.4 PCR ................................................................................................... 20 2.7.5. 2.7.5 Probe-tag based genotyping .............................................................. 21 2.7.6. 2.7.6 Sanger sequencing ............................................................................. 22 2.7.7. 2.7.7 Real-time qualitative polymerase chain reaction ............................... 22 2.7.8. 2.7.8 SNP arrays ......................................................................................... 22 2.8. 2.8 Genotyping vs. gene expression ....................................................................... 23 2.8.1. 2.8.1 Call rate and accuracy ....................................................................... 23 3. 3 Comparative protein modeling and molecular docking ................................................... 24 3.1. 3.1 Introduction ...................................................................................................... 24 3.1.1. 3.1.1 The protein structure gap ................................................................... 24 3.1.2. 3.1.2 Methods of protein modeling ............................................................ 25 3.2. 3.2 Comparative protein modeling ......................................................................... 26 3.2.1. 3.2.1 Steps of homology modeling ............................................................. 26 3.2.2. 3.2.2 Tools for homology modeling ........................................................... 30 3.3. 3.3 Molecular docking ............................................................................................ 32 3.3.1. 3.3.1 Protein-ligand interaction predictions ............................................... 33 iii Created by XMLmind XSL-FO Converter. Bioinformatics 3.3.2. 3.3.2 Protein-biomacromolecule interaction predictions ............................ 34 4. References ........................................................................................................................... 34 5. 4 Methods of determining structure of proteins and protein structure databases ................ 36 5.1. 4.1 Introduction ...................................................................................................... 36 5.1.1. 4.1.1 Protein identification tools ................................................................ 36 5.1.2. 4.1.2 Simple protein analyses ..................................................................... 37 5.1.3. 4.1.3 Levels and problems of protein structure predictions ....................... 37 5.2. 4.2 Experimental methods to determine the secondary structure of proteins ......... 38 5.2.1. 4.2.1 Protein circular dichroism (CD) ........................................................ 38 5.2.2. 4.2.2 Synchrotron radiation circular dichroism (SRCD) ............................ 39 5.3. 4.3 Experimental methods to determining atomicstructures of proteins ................. 40 5.3.1. 4.3.1 Protein X-ray crystallography ........................................................... 41 5.3.2. 4.3.2 Protein NMR spectroscopy ............................................................... 42 5.3.3. 4.3.3 Protein electron microscopy, electron diffraction and electron crystallography ..................................................................................................... 44 5.3.4. 4.3.4 Protein neutron crystallography ........................................................ 44 6. 5 Quantitative models of the functional effects of genetic variants .................................... 45 6.1. 5.1 Introduction ...................................................................................................... 45 6.2. 5.2 Variants ............................................................................................................. 45 6.2.1. 5.2.1 SNP, indel ......................................................................................... 45 6.2.2. 5.2.2 Alternative splicing ........................................................................... 46 6.3. 5.3 Levels of regulation .......................................................................................... 46 6.4. 5.4 Different regulatory elements ........................................................................... 46 6.5. 5.5 microRNA .......................................................................................................