1. Monday, November 8, 2:30:07 PM  Ontology is the philosophical study of the nature of being, existence or reality as such, as well as the basic categories of being and their relations.  Traditionally listed as a part of the major branch of philosophy known as metaphysics.  Ontology deals with questions concerning whether entities exist and how such entities can be grouped, related within a hierarchy, and subdivided according to similarities and differences. What is ontology? Lec 08 So what does that mean?  From a practical view, ontology is the representation of something we know about. “Ontologies" consist of a representation of things, that are detectable or directly observable, and the relationships between those things.

2. Monday, November 8, 2:30:07 PM What is gene ontology? Lec 08 In this study, we report the isolation and molecular characterization of the B. napus PERK1 cDNA, that is predicted to encode a novel receptor-like kinase. We have shown that like other plant RLKs, the kinase domain of PERK1 has serine/threonine kinase activity, In addition, the location of a PERK1-GTP fusion protein to the plasma membrane supports the prediction that PERK1 is an integral membrane protein …these kinases have been implicated in early stages of wound response…

3. Monday, November 8, 2:30:07 PM  There are lots of papers to read. What is gene ontology? Lec 08  More and more papers…  There are lots of genes.  More and more genes... Microarray data shows changed expression of thousands of genes. How will you spot the patterns?  How will you ever find what you want?

4. Monday, November 8, 2:30:07 PM What is gene ontology? Lec 08  Can the computer gurus help? They are trying with ontologies!  Gene ontology is a way to capture knowledge in a written and computable form.  The Gene Ontology Project began in about 2001, started by several model organism databases.  GO built for annotation of genes and proteins and basically it is applicable to any species.  Gene Ontology widely adopted.

5. Monday, November 8, 2:30:07 PM  The Gene Ontology (GO) provides a controlled dictionary of terms for describing gene product characteristics and gene product annotation data.  GO is divided into three sub-vocabularies: Biological process: broad series of actions, can either be at the level of the cell or organism e.g. cell cycle, development, metabolic processes, regulation, response to stimulus, signaling, transport and transporters. Molecular function: direct activities e.g. DNA binding, hormone activity, transcription factor activity, cytochrome-c oxidase activity, growth factor activity, oxidoreductase activity. Cellular component: site of action e.g. nucleus, membrane, extracellular, mitochondria, E.R., Golgi.  Terms are organized in hierarchical What is gene ontology? Lec 08 Node has children, can be clicked to view children

6. Monday, November 8, 2:30:07 PM Gene Ontology Lec 08  GO available on different web hosting service: http://www.geneontology.org/, http://www.ebi.ac.uk/QuickGO/, http://amigo.geneontology.org/cgi-bin/amigo/go.cgi

7. Monday, November 8, 2:30:07 PM ISS: Inferred from Sequence IDA: Inferred from Direct Assay IPI: Inferred from Physical Interaction IMP: Inferred from Mutant Phenotype IGI: Inferred from Genetic Interaction IEP: Inferred from Expression Pattern TAS: Traceable Author Statement NAS: Non-traceable Author Statement IC: Inferred by Curator ND: No Data available IEA: Inferred from electronic annotation  Evidence types Gene Ontology Lec 08

8. Monday, November 8, 2:30:07 PM Gene Ontology Lec 08

9. Monday, November 8, 2:30:07 PM What is Ontology? Lec 08 Is_a relationship Part_of relationship

10. Monday, November 8, 2:30:07 PM What is Ontology? Lec 08

11. Monday, November 8, 2:30:07 PM Lec 08 1. 2. 1. 2. What is Ontology?

12. Monday, November 8, 2:30:07 PM What is Ontology? Lec 08

13. Monday, November 8, 2:30:07 PM Multiple sequence alignment : purpose and applications  Bay now, based on orthology, we have annotated genes, proteins or RNA molecules. Is there anything further we can do at this point? Phylogenetic reconstructions: some methods to generate of a phylogenetic tree require a multiple sequence alignment as input. Generation of a sequence family or domain model: such models are called consensus sequences, weight matrices, profiles, hidden Markov model, etc. Sequence similarity search with family or domain models is more sensitive than single sequence search. Assembly of a contig DNA sequences from single sequence reads: complete mRNA, chromosome, or genome sequences are obtained from error-prone single read sequences by a specialized multiple alignment procedure. Lec 08

14. Monday, November 8, 2:30:07 PM  Multiple sequence alignment (MSA) is a bioinformatics procedure in which at least three protein, DNA (deoxyribonucleic acid) or RNA (ribonucleic acid) sequences are aligned to each other.  This produces a visual pattern where sequences that are present in a set of sequences become matched within a single block of color.  Usually, the sequences come from different organisms or species, thus allowing us to determine whether and what type of relationship exists between the sequences. Lec 08 Multiple sequence alignment Completely conserved = asterisk (*), Highly conserved = colon (:), Conserved = period (.).The red box indicate a highly conserved block. These blocks are often functionally important positions.

15. Monday, November 8, 2:30:07 PM Global alignment in which entire sequences are aligned at the same time using extension of dynamic programming. Local alignment in which conserved local regions are found by statistical methods. Lec 08  Why is multiple sequence alignment a computationally hard problem? Because optimal pair-wise alignments from a set of sequences are not necessarily compatible with each other and thus cannot be combined in a single multiple alignment.  There are several tools to generate MSA, however they are not identical. Multiple sequence alignment: statement of the problem  Types of multiple sequence alignment

16. Monday, November 8, 2:30:07 PM Making a multiple sequence alignment  Identify a set of related sequences by Gene Ontology Project or Blast Choose a method: www.ebi.ac.uk/clustalwClustalWPopularwww.ebi.ac.uk/clustalw http://align.genome.jp http://www.ch.embnet.org/software/ClustalW.html www.tcoffee.orgT-CoffeeAccuratewww.tcoffee.org www.drive5.com/muscle/MuscleFastwww.drive5.com/muscle/ www.tcoffee.orgM-CoffeeConsensuswww.tcoffee.org Lec 08

17. Monday, November 8, 2:30:07 PM Lec 08 ClustalW2 is a MSA program designed strictly for the analysis of proteins or DNA, not RNA. It is hosted by the European Bioinformatics Institute (EBI) and is provided as either a webpage form or downloaded as a software package. Making a multiple sequence alignment

18. Monday, November 8, 2:30:07 PM Difficulties of RNA