1. Online Counseling Resource YCMOU ELearning Drive… School of Architecture, Science and Technology Yashwantrao Chavan Maharashtra Open University, Nashik – 422222, India

2. OC-SBI083-CP1-01 Introduction Programmes and Courses  SBI083-CP1_U01_01

3. School of Science and Technology, Online Counseling Resource… Credits  Academic Inputs by Sonali Alkari MSc (Botany), P.G. D.C. Bio-Informatics sonalisa_alkari@yahoo.com

4. School of Science and Technology, Online Counseling Resource… © 2007, YCMOU. All Rights Reserved.4 How to Use This Resource  Counselor at each study center should use this presentation to deliver lecture of 40-60 minutes during Face-To-Face counseling.  Discussion about students difficulties or tutorial with assignments should follow the lecture for about 40-60 minutes.  Handouts (with 6 slides on each A4 size page) of this presentation should be provided to each student.  Each student should discuss on the discussion forum all the terms which could not be understood. This will improve his writing skills and enhance knowledge level about topics, which shall be immensely useful for end exam.  Appear several times, for all the Self-Tests, available for this course.  Student can use handouts for last minutes preparation just before end exam.

5. School of Science and Technology, Online Counseling Resource… © 2007, YCMOU. All Rights Reserved.5 Learning Objectives  After studying this module, you should be able to: Explain what is perl State reasons for perl usage in bioinformatics. Explain what is bioperl. State uses of bioperl

6. School of Science and Technology, Online Counseling Resource… Introduction:1  There are currently over 2000 computer languages.  The very first programming languages were “machine languages(I.e. coded bytes).  The next programming languages were the “assembly languages”.  The next group of languages are “higher level languages” which allowed the programmer to work more conceptually.

7. School of Science and Technology, Online Counseling Resource… Introduction:2  The programs written in higher level languages could be translated into machine language (by another program called a compiler) or interpreted(by program called an interpreter).  A few of the most influential high level languages are Fortran, Cobol, C, Pascal, C, C ++, Perl, Java  Bioinformatics, a rapidly evolving discipline, is the application of computational tools and techniques to the management and analysis of biological data.

8. School of Science and Technology, Online Counseling Resource… Introduction:3  Programming skills are now in strong demand in biology research and development.  A large part of computational biology consists if routine  Text-processing tasks such as string manipulation, regular expression matching, file parsing and data format interconversion.  It also involves manipulating the output from sequence analysis programs such as BLAST, FASTA.

9. School of Science and Technology, Online Counseling Resource… Introduction:4  Also an interaction with different sequence databases such as Pfam, Genbank/EMBL/DDBJ has to be built up.  Perl is ideally suited for bioinformatics as its involves writing programs that left through mountains of data to extract just the information you need.  Perl is the most obvious choice for patterns detection data, especially string of text, with its highly developed capacity.

10. School of Science and Technology, Online Counseling Resource… Perl:Practical Extraction and Report Language  Perl means the Practical Extraction and Reporting Language.  Perl is a popular programming language that’s extensively used in in areas such as bioinformatics and web browsing.  Perl has become popular with biologists because it’s so well suited to several bioinformatics tasks.  Perl is an application just like other application install on computer.

11. School of Science and Technology, Online Counseling Resource… Why use Perl in Bioinformatics :1  Perl has a low learning curve. This means you can get started easily, without having master a large body of information before writing useful programms.  Perl has certain features that simplifies several common bioinformatics task.  Perl makes it easy to process and manipulate long sequences such as DNA and proteins.

12. School of Science and Technology, Online Counseling Resource… Why use Perl in Bioinformatics:2  Perl makes it convenient to write a program that controls one or more other program.  Perl is used to put biology research labs, and their results, on their own dynamic web sites.  Another important benfit of using Perl for biological research is the speed with which a programmer can write typical Perl program.  Perl takes less programming time to extract data than with C or Java.

13. School of Science and Technology, Online Counseling Resource… Why use Perl in Bioinformatics:3  The smother integration of the health of the existing perl code for bioinformatics on the Unix based system, cross platform portability, incredibly enthusiastic user community user community.  Biological data is stored in enormous databases and file text., With highly developed capacity to detect patterns in data, perl is the best choice for data extraction.

14. School of Science and Technology, Online Counseling Resource… Why use Perl in Bioinformatics:4  Perl has a flexible syntax, or grammar.  Programming problems requiring many lines of code in other languages may be solved in a few lines of perl.

15. School of Science and Technology, Online Counseling Resource… Bioperl Project:1  The bioperl project ia a project aimed at making many of the bioinformatics tasks simpler through the creation of a set of software modules to help manipulate, manage and interpret data.  Bioperl has a number of sister languages project including Biojava and Biopython projects as well as format and languages bridges in the BioXMl and BIOCorba projects.

16. School of Science and Technology, Online Counseling Resource… Bioperl Project:2  All these projects are open-source software designed to give bioinformatics programmers an easy interface for solving problem.  Bioperl is used as a basic for managing biological information by numerous groups doing bioinformatics.  The most prominent is project HGP (Human Genome Project), Ensembl etc.

17. School of Science and Technology, Online Counseling Resource… Bioperl Project:3  Ensembl uses bioperl as the foundation for creating objects such as Exon, Gene, transcript, Clone, Contig are all built from bioperl objects and used to manipulate and annotate sequence.  In HGP several perl scripts were used to analyze new DNA sequence and also used for format conversion, manipulation, laboratory management etc.

18. School of Science and Technology, Online Counseling Resource… Some specific BioPerl projects are-  Sequence objects: sequence manipulation and lightweight analyses  Sequence similarity Search:genetic sequence similarity searches  Sequence DB Access:retrieving sequence objects from databases  Sequence alignment: both dumb and clever representation of alignments and methods for making alignments  Sequence Annotation:attaching annotation on sequences  Structure Objects: a protein structure objects.

19. School of Science and Technology, Online Counseling Resource… What You Learn…  You have learnt :  What is Perl  Features of Perl  Uses of perl in bioinformatics  What is bioperl and its application

20. School of Science and Technology, Online Counseling Resource… Critical Thinking Questions 1.Write a short note on perl. 2.Write in short note on bioperl. © 2007, YCMOU. All Rights Reserved.20

21. School of Science and Technology, Online Counseling Resource… Hints For Critical Thinking Question 1.Define perl and state why it use in bioinformatics. 2.Define bioperl and give its uses. © 2007, YCMOU. All Rights Reserved.21

22. School of Science and Technology, Online Counseling Resource… Study Tips:Books  Beginning Perl by Simon Cozens, Peter Wainwright. 700 pages. Wrox Press Inc. (May 25, 2000). Beginning Perl  Impatient Perl by Greg London (Feb 7, 2004). Extreme Perl by Robert Nagler Impatient Perl Extreme Perl  MacPerl: Power & Ease by Vicky Brown and Chris Nandor. 372 pages. (1998). MacPerl: Power & Ease  Picking Up Perl by Bradley M. Kuhn and Neil Smyth. self published. second edition. (July 2005). Picking Up Perl

23. School of Science and Technology, Online Counseling Resource… Study Tips:Web Resources www.en.wikipedia.org Microsoft Encarta Encyclopedia http://www.perl.org/ http://en.wikibooks.org/wiki/Programming:Perl_W ebsiteshttp://en.wikibooks.org/wiki/Programming:Perl_W ebsites http://en.wikibooks.org/wiki/Programming:Perl_W ebsites http://cpan.perl.org/

24. School of Science and Technology, Online Counseling Resource… Community Web Sites  Planet Perl - an aggregation of selected perl journals Planet Perl  use Perl; - read community news and personal journals, or start your own journal use Perl;  Perl Monks - the wisdom of the Monks can guide you on your Perl Quests Perl Monks  perl.org - your current location perl.org  the Perl Apprenticeship Site the Perl Apprenticeship Site

25. School of Science and Technology, Online Counseling Resource… End of the Presentation Thank You