R V COLLEGE OF ENGINEERING, BANGALORE 560059

(Autonomous Institution under VTU, Belgaum)

Department Instrumentation Technology

FMTH0301 Rev. 2.0

Course Plan
Cover Page: Course Overview Semester: VII
Course Title: Bioinformatics and Applications Total Contact Hours:42 hrs SEE Marks: 100 Lesson Plan Author: Tabitha Janumala Checked By:

Year: 2010-11
Course Code: 07IT763 Duration of SEE: 3 hrs CIE Marks: 100 Date: 30/08/2010 Date:

Prerequisites: Biological knowledge of RNA , DNA and Proteins, HTML, XML, PERL Languages. Course Overview: Bioinformatics combines practical insight for assessing bioinformatics technologies, practical guidance for using them effectively, and intelligent context for understanding their rapidly evolving roles such as: Technologies that enable researchers to collaborate more effectively Fundamental concepts, state-of-the-art tools, and "on the horizon" advances Bioinformatics information infrastructure, including GENBANK and other Web-based resources Very large biological databases: object-oriented database methods, data mining/warehousing, knowledge management, and more 3D visualization: exploring the inner workings of complex biological structures Advanced pattern matching techniques, including microarray research and gene prediction Event-driven, time-driven, and hybrid simulation techniques

Course Learning Objectives: 1. 2. This course aims at introducing the fundamental concepts of organization of DNA and Protein sequences. The objective is intended for students to understand the concepts of statistical tools and algorithms to analyze and determine relationships between biological data sets, such as macromolecular sequences, structures, expression profiles and biochemical pathways. 3. 4. This course gives the knowledge of programming in different languages such as HTML, XML and Perl. This course imparts the basic concepts and ideas of methods of Phylogenetic Analysis

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R V COLLEGE OF ENGINEERING, BANGALORE 560059

(Autonomous Institution under VTU, Belgaum)

Department Instrumentation Technology

Course Content
Course Code: 07IT763 Course Title Teaching Hours: 40 L-T-P: 4-1-1 CIE: 100 SEE: 100

PART A
The Central Dogma: Watsons definition, information flow, from data to knowledge, Convergence, the organization of DNA, the organization of Proteins. XML (Bio XML) for Bioinformatics: Introduction, Differences between HTML and XML, fundamentals of XML, fundamentals of XML namespaces. Introduction to DTDs, Document type Declarations, Declaring elements, declaring attributes, working with entities XML Schemas, Essential Concepts, working with simple types, working with complex types, Basic namespaces issues. Perl (Bioperl) for Bioinformatics : Representing sequence data, program to store a DNA sequence, concatenating DNA fragments, Transcription, Calculating the reverse complement in Perl, Proteins, files, reading proteins in files, Arrays, Flow control, finding motifs, counting Nucleotides, exploding strings into arrays, operating on strings, writing to files, subroutines and bugs. 10 Hours 6 Hours 3 Hours

PART B Databases : Flat file, Relational, object oriented databases, object Relational and Hypertext, Data life cycle, Database Technology Sequence Alignment Algorithms: Biological motivations of sequence analysis, the models for sequence analysis and their biological motivation, global alignment, local alignment, End freespace alignment and gap penalty, Sequence Analysis tools and techniques. PART C Phylogenetic Analysis : Introduction, methods of Phylogenetic analysis, distance methods, the neighbor- Joining (NJ) method, The Fitch/ Margoliash method, character-based methods, Other methods, Tree evaluation and problems in phylogenetic analysis. Clustering: Protein structure visualization and Protein structure prediction Reference Books 1. 2. 3. 4. Bioinformatics Methods and Applications, S.C.Rastogi, N. Mendiratta. XML for Bioinformatics CERAMI. Beginning Perl for Bioinformatics James D. Tisdall. Bioinformatics Computing Bryan Bergeron, M.D 4 Hours 6 Hours 10 Hours 9 Hours

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R V COLLEGE OF ENGINEERING, BANGALORE 560059

(Autonomous Institution under VTU, Belgaum)

Department Instrumentation Technology

Evaluation Scheme CIE Scheme Assessment 2 Quiz 2 Internals Total Weightage in Marks 20 30 50

Best out of 2 Quiz and 2 Internals will be considered for CIE marks. Course Unitization for Internals and Semester End Examination
No. of Questions in Part 1 2 A 3 Chapter The Central Dogma XML (Bio XML) for Bioinformatics Perl (Bioperl) for Bioinformatics 4 B 5 Databases Sequence Alignment Algorithms 6 C 7 Phylogenetic Analysis Clustering 4 6 ----4 4 1 2 9 10 -4 10 3 -4 1.5 1.5 Teachin g Hours 3 6 3 -1.5 Internals I 2 Internals II -Compensator y Internals No. of Questions in SEE 0.5 1.0

Note: Eight questions will be asked in the internals out of which student should answer five questions. Each question carries 10 Marks. Faculty In-charge Tabitha Janumala Date: 30/08/2010 Head of Department

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R V COLLEGE OF ENGINEERING, BANGALORE 560059

(Autonomous Institution under VTU, Belgaum)

Department Instrumentation Technology

Chapter wise Plan PART A

Course Code and Title: Bioinformatics and Applications/07IT763 Chapter Number and Title: 1 The Central Dogma Planned Hours: 3 hrs

Learning Objectives 1. It explores the relationship of molecular biology and bioinformatics to computer science 2. How the purview of computational bioinformatics necessarily extends from the molecular to the clinical medical level. Lesson Schedule Class No. Portion covered per hour 1. Watsons definition, Information flow, 2. From data to knowledge, convergence 3. Organization of dna, the organization of proteins.

Model Questions 1.

2. 3. 4. 5.

With a neat diagram illustrate the central dogma of molecular biology? Explain the process of mRNA synthesis? With a neat diagram explain the DNA structure? Distinguish between RNA and DNA? With a neat block diagram explain the information flow in biological applications?

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R V COLLEGE OF ENGINEERING, BANGALORE 560059

(Autonomous Institution under VTU, Belgaum)

Department Instrumentation Technology

Course Code and Title: Bioinformatics and Applications/07IT763 Chapter Number and Title: 2 XML (Bio XML) for Bioinformatics Learning Objectives At the end of this chapter student should be able to: 1. 2. 3. Provides an introduction to XML programming briefs about the DTDs and the XML Schemas. It gives the idea of differences between HTML and XML It explains the concept of declaring elements and attributes. Planned Hours: 6 hrs

Lesson Schedule Class No. Portion covered per hour 1. Introduction, Differences between HTML and XML, 2. Fundamentals of XML, fundamentals of XML namespaces. 3. Introduction to DTDs, 4. Document type Declarations, Declaring elements, declaring attributes 5. Working with entities XML Schemas, 6. Essential Concepts, working with simple types, working with complex types, Basic namespaces issues. Model Questions

1.
2.

3.
4.

5. 6.

7.
8.

9. 10. 11. 12.

Discuss the advantages and disadvantages of XML? With an example explain the syntax of different types of element declaration? Define XML entity? Explain different types of classification? When a XML document is said to be well formed? What is the necessity of CDATA instruction? Write a XML program to create an application of genome as element, chromosome, gene, nitrogen bases of DNA, protein name and organism as attributes. Illustrate with example the DTD syntax for defining XML attributes. Why do we need XML namespaces? With an example give the syntax for declaring the namespaces? Distinguish between DTDs and XML Schemas? With appropriate examples explain any five XML Schema data types. What is a facet? Briefly explain the Pattern facet and enumeration facet?

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R V COLLEGE OF ENGINEERING, BANGALORE 560059

(Autonomous Institution under VTU, Belgaum)

Department Instrumentation Technology

Course Code and Title: Bioinformatics and Applications/07IT763 Chapter Number and Title: 3 : Perl (Bioperl) for Bioinformatics Learning Objectives Provides an introduction to Perl programming. 1. 2. 3.
4.

Planned Hours: 6 hrs

To store the DNA sequences Concatenate two DNA fragments Transcription To calculate the reverse compliment of a DNA sequence.

Lesson Schedule Class No. Portion covered per hour 1. Representing sequence data, program to store a DNA sequence, 2. Concatenating DNA fragments, transcription, 3. Calculating the reverse complement in PERL, 4. Proteins, files, reading proteins in files, arrays, flow control, 5. Finding motifs, counting nucleotides, exploding strings into arrays, 6. Operating on strings, writing to files, subroutines and bugs.

Model Questions

1. 2. 3. 4. 5. 6.

What are the advantages of using Pear language in bioinformatics? Write a subroutine to append ACGT to DNA sequence using Perl language. What is the reverse compliment of the following sequence ACGGAGGACGGGAAA Write a Perl program to calculate the reverse compliment of the above DNA sequence. Write a Perl program for transcription of DNA to RNA and explain every instruction. Write a Perl program to declare an array initialized with four scalar values such as A, G, C and T. then i) Take an element off the end of an array. ii) Take a base off of the beginning of the array. 7. Write a Perl program to determine the frequency of nucleotides. 8. Write a Perl program to search for the motifs.

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R V COLLEGE OF ENGINEERING, BANGALORE 560059

(Autonomous Institution under VTU, Belgaum)

Department Instrumentation Technology

PART B

Course Code and Title: Bioinformatics and Applications/07IT763 Chapter Number and Title: 4. Databases Learning Objectives Planned Hours: 9 hrs

1. 2. 3. 4.

It deals with the creation of the database. It gives the idea of differences between different types of databases. It explains about the acquisition of the biological data. It gives the idea of how to archive the biological data.

Lesson Schedule Class No. Portion covered per hour 1. Flat file, Relational, 2. object oriented databases, 3. object Relational and Hypertext, 4. Data life cycle, Database Technology, 5. Database Architecture, 6. Database Management Systems and Interfaces Model Questions

Define Database Management System (DBMS).Give any four features of DBMS. 2. Explain the concept of database management system using the application of metadata, information and data. 3. List out any 10 key issues of bioinformatics in the archival process.
1.

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R V COLLEGE OF ENGINEERING, BANGALORE 560059

(Autonomous Institution under VTU, Belgaum)

Department Instrumentation Technology

Course Code and Title: Bioinformatics and Applications/07IT763 Chapter Number and Title: 5 Sequence Alignment Algorithms Learning Objectives 1. 2. 3. 4. It deals with the different alignment techniques of DNA sequences. The difference between local and global alignment is known. It explains about the biological motivation of sequence analysis. It deals with how to improve the score of sequence alignment. Planned Hours: 5 hrs

Lesson Schedule Class No. Portion covered per hour 1. Biological motivations of sequence analysis, 2. The models for sequence analysis and their biological motivation, 3. Global alignment, 4. Local alignment, 5. End free-space alignment 6. And gap penalty, 7. Sequence analysis tools and techniques. Model Questions

1. List out the biological motivation of sequence analysis. Briefly explain the sequence analysis tools and techniques. 2. Find the scoring for the following sequences. Sequence1 : M N O P V P O N M Sequence2 : N O P V P O N M N Using lookup table show how we can improve the scoring for the sequences 1 and 2? 3. Mention the major variants of biosequences alignment techniques. Distinguish between local and global alignment techniques. 4. Give an example for an end free space sequence alignment and the inter relationship between match score, mismatch score & Gap penalty.

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R V COLLEGE OF ENGINEERING, BANGALORE 560059

(Autonomous Institution under VTU, Belgaum)

Department Instrumentation Technology

PART C
Course Code and Title: Bioinformatics and Applications/07IT763 Chapter Number and Title: 6 Phylogenetic Analysis Learning Objectives 1. 2. 3. It briefs about the sequence alignment and understanding the evolutionary relationships. It deals with BLAST and FASTA the most versatile and popular tools. Planned Hours: 6 hrs

Lesson Schedule Class No. Portion covered per hour 1. Introduction, methods of phylogenetic analysis 2. Distance methods, 3. The neighbor- joining (nj) method, 4. The Fitch/ Margoliash method, 5. Character-based methods, Other methods, 6. Tree evaluation and problems in phylogenetic analysis.

Model Questions 1. 2.

3. 4. 5.

Define phylogeny. Illustrate Phylogenetic trees with an example of a rooted tree of four taxa showing branch length. Define the following terms: i) Branch ii) Topology iii) Branch Length iv) Root v) Distance Scale Illustrate with an example the character based Phylogenetic analysis methods. Differentiate between NJ and Fitch Margoliash method. Explain the tree evaluation methods?

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R V COLLEGE OF ENGINEERING, BANGALORE 560059

(Autonomous Institution under VTU, Belgaum)

Department Instrumentation Technology

Course Code and Title: Bioinformatics and Applications/07IT763 Chapter Number and Title: Clustering Planned Hours: 4hrs

Learning Objectives 1. It deals with the prediction of gene s in genome sequences and microarray analysis and technologies. Lesson Schedule Class No. Portion covered per hour 1. 2. Protein structure visualization Protein structure prediction

Model Questions

What is clustering? How is it classified? With an example briefly illustrate the agglomerative clustering and Hierarchical clustering techniques. 3. With a neat diagram explain the four types of protein visualization?
1. 2.

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