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Unit No. 1

PERL for Bioinformatics LTPC: 3 0 2 4 1.0.1 Introduction to Algorithms This course gives the students a basic understanding of Perl programming and serves as a basic foundation for learning Bioperl. The various functions of Perl have been dealt in detail for a better understanding of the students. The students will be able to handle various biological problems using perl programming. Student will learn: - To analyze any given DNA or Protein string. - Rectify and analyze the errors generated in PERL programs. - Deal with the files and folders of various biological databases. - Learn how to use Bioperl. Number of hours: 9 Biology and Computer Science

Organization of DNA - the organization of proteins - in silico - limits to computation. Getting started with PERL: a low and long learning curve - perl benefits - installing perl on your computer - how to run perl programs - text editors - finding help Unit No. 2 Number of hours: 9 The Art of Programming Individual approaches to programming - edit-run-revise (and save) - an environment of programs - programming strategies -the programming process. Sequences and strings representing sequence data - a program to store a dna sequence - concatenating dna fragments - transcription: DNA to RNA. Unit No. 3 Number of hours: 9 Motifs and Loops Flow control - code layout - finding motifs - counting nucleotides - exploding strings into arrays - operating on strings - writing to files. Subroutines and Bugs: subroutines scoping and subroutines - command-line arguments and arrays - passing data to subroutines - modules and libraries of subroutines. Unit No. 4 Number of hours: 9 Mutations and Randomization Random Number Generators - A Program Using Randomization - A Program to Simulate DNA Mutation - Generating Random DNA - Analyzing DNA. The Genetic Code : Hashes - Data Structures and Algorithms for Biology - The Genetic Code - Translating DNA into Proteins. Restriction Maps and Regular Expressions : Regular Expressions Unit No. 5 Number of hours: 9 Using Data Bank GenBank : genbank files - genbank libraries - separating sequence and annotation - parsing annotations - indexing genbank with DBM. Protein Data Bank Files and folders - pdb files - parsing pdb files - controlling other programs. BLAST : Obtaining BLAST Text Books James Tisdall, Beginning Perl for Bioinformatics First Edition 2001. References 1. Wall, LT. Christiansen, and J. Orwant, O'Reilly. Programming Perl, 2000. 2. Gibas, C and P. Jambeck, O'Reilly. Bioinformatics Computer Skills. 2001. Announced / Unannounced Quiz / tests, Assignments and Written Examination List of Experiments Programming basics commands and text editors Translation of DNA to Proteins Storing and concatenating DNA fragments and proteins Counting to nucleotides and proteins and writing to files

Mode of Evaluation

DNA mutation and generating random DNA Analysis of DNA and Proteins. Writing new PERL programs for de novo DNA / protein analysis Recommended by the Board of Studies on 29 September 2009 Date of Approval by the Academic Council