1. Overview of Bioinformatics 1 Module Denis Manley.

2. Contact Details Lecturer Name: Denis Manley Room number: KE-1-013a Email : denis.manley@dit.iedenis.manley@dit.ie Website: www.comp.dit.ie/dmanleywww.comp.dit.ie/dmanley Phone: 01 402 4949

3. What is bioinformatics Bioinformatics is the use of computers and computational methods to analyse large sets of molecular biological data that is used for : – The investigation of “living organisms” and their evolution. – The discovery of genes, gene regulation; genetic networks and protein functionality, which can be used to understand: human disease; human development (conception to adulthood) etc. – the results of which can facilitate our understanding of diseases like cystic fibrosis; suggest therapies; and the development of cures such as drug development, viral therapy…

4. Reading DNA novels: “bioinformatics” Analysing large sets of data is “equivalent” to reading and understanding a book (similar to Computational linguistics): – The first step in reading a book involves looking at letters [ including spaces and punctuation] to determine the words. Bioinformatics is the reading of DNA (alphabet referred to by letters ATGC) and determining location of important regions of the sequence; e.g. genes, gene “expression” control regions….

5. Reading DNA novels: “bioinformatics” – The next step in reading involves determining if the words are nouns/verbs/adverbs etc… In general each language has rules: “what are these rules” – Bioinformatics involves determining what the “important elements” correspond to: e.g. genes; gene promoters…. – However, clearly the rules to determine “genes” and other elements are no as well defined as in a natural language and more importantly are constantly being modified and updated.

6. Reading DNA novels: “bioinformatics” – syntax: – The next step in determining the sequence of the words.; e.g. should it be“what are the rules of english grammar”; are “what the rules of grammar english“ – Bioinformatics involves determining the sequence of “important elements”; e.g. promoter are “upstream of genes and not the other way around.

7. Reading DNA novels: “bioinformatics” – Symantics: – What does the set of words (sentence) mean. “what is your purpose?” what processes do humans use to interpret this sentence – Bioinformatics attempts to analyse the function of DNA/genetic sequences by: e.g. comparing the sequences to sequences whose function is already known. By converting the sequence into its equivalent “protein” and comparing it to known proteins determining 3-D structure of proteins and looking for known structural components.

8. Reading DNA novels: “bioinformatics” Bioinformatics also focuses on the IT aspects of the discipline such as: – Setting up databases – Writing code to perform analysis – Determining and Utilisation of known computational techniques to improve analysis of the biological data. Bioinformatics, covers a very large area but this particular module will focus on the “computational analysis of genetic systems” and will be referred to as Bioinformatics 1.

9. Bioinformatics 1: module syllabus. Part 1:Introduction to fundamental of genetic systems: Principles of inheritance and evolutions: essential criteria for our evolution and existence. Basic Molecular cell biology: DNA, Genes and Amino acids (proteins). The relationship between a gene and its physical manifestation (proteins); The central “dogma” of Genetics: DNA -> RNA- >Proteins Introduction to structural elements of genetic systems Gene “expression” regulation

10. Bioinformatics 1: module syllabus. Part 2: Fundamentals of “ bioinformatics” PERL: a common scripting language used in the field of bioinformatics Fundamentals of Perl: read/write, loops…. Fundamental Perl data structures: “bioinformatics“ data files; dynamic arrays and hash tables. Perl Pattern matching techniques used in bioinformatics: searching for a pattern (e.g. ATG); extract a pattern from a sequence; substitute one pattern for another (e.g. replace T with a U) Create perl sub-routines and Perl modules and use them in other perl programs Development of “basic” bioinformatics data sequences analytical tools using perl and core computational algorithms [these algorithms will be covered in the computational element of the module].

11. What is bioinformatics – Part 3: Introduction to online bioinformatics resources; How and where to obtain “bioinformatics” DNA data sequences and data relevant to these sequences Explanation of the different elements of these data sets “data annotation” or (meta data). Fundamentals of common online DNA analytical tools (such as sequence alignment measurement )

12. What is bioinformatics Part 3: – Computational bioinformatics techniques, including Artificial intelligent techniques, used to: Principles of DNA pattern matching: global/local/multiple Principles of Align DNA sequences: e.g. Pairwise alignment Application of alignment principles using basic computational methods Reconstruct genomes (large DNA sequences) using “shot- gun” alignment techniques Principles of searching for “matching” DNA (gene) sequences in large online databases. How to utilise and interpret findings of DNA database searches: e.g. gene functionality and evolutionary gene markers.

13. Assignment and exam 1 Assignment (40%): – Developing an application to analyse “small” DNA data sequences – A report discussing the findings of the applications when applied to known DNA sequences Exam: question 1 + 2 out of 4 other question (60%) – Question 1 compulsory: Perl programming. – Other questions related to other areas in the module.

14. Proposed schedule Week 2 to Week 6 (Wednesday 16:00 to 18:00): “Part 1 Fundamental of genetic systems.” Week 2 to Week 6 (Monday 9:00 to 11:00) – Fundamentals of perl Week 7 review week [submit assignment part 1]

15. Proposed schedule Week 8 to Week 12 (Wednesday 16:00 to 18:00): “Computational techniques and their application to bioinformatics” Week 8 to Week 12 (Monday 9:00 to 11:00) – Online bioinformatics databases and analytical applications (approx 2 weeks). – Development of fundamental computational applications using perl (approx 3 weeks) Week 10 submission of assignment part 2 Week 13 review of course and sample exam paper

16. Assignment content Assignment 1: – A report on the analysis on the biological impact of developing “ a bioinformatics applications. – Development of the fundamental functionality of the application based on the findings of the report Assignment 2: – Using the application from assignment 1: Analysis and development of the analytical component “computational analysis” of the application. – A report on the findings of applying the final application to a given dataset obtained from online bio-informatic databases.