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Unit-1 Introduction to Bioinformatics

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Course : MSc BT

Semester : III

Subject Code : MBT 30

Subject !ame : Com"utationa# Bio#o$%

Unit number : 1

Unit Tit#e : Introduction to Bioinformatics

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Unit-1 Introduction to Bioinformatics

Objecti&es

After studying this unit, you should be able to:

describe the scope and application of bioinformatics

explain biological patterns and familiarize yourself with the techniques used to

detect it

discuss the concept of integration of database

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Unit-1 Introduction to Bioinformatics

Introduction

ioinformatics ! An o"er"iew

ioinformatics s#ill sets for a biologist

$etecting %atterns in iological &equences

&ummary

'ecture Out#ine

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Introduction

'ecall a famous quote by Haro#d Mar(o)it*

regarding the relationship between computerscience and biology ! +Com"uters are tobio#o$% ),at mat,ematics is to ",%sics.

%ast few decades, ma(or ad"ances in the fieldof molecular biology, coupled with ad"ances in

genomic technologies led to an explosi"egrowth in the biological information generatedby the scientific community)

&urge of genomic information has led to anabsolute requirement for computerized

databases to store, organize, and index thedata, and for specialized tools to "iew andanalyze the data

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Unit-1 Introduction to Bioinformatics

Bioinformatics / n o&er&ie)

ioinformatics defined as the application of Information technology to

store, organize and analyze the "ast amount of biological data *

a"ailable in the form of sequences and structures of proteins and

nucleic acids)

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Unit-1 Introduction to Bioinformatics

ims of bioinformatics

+i -rganization of data

+ii $e"elopment of Analysis tool

+iiiAnalysis of $ata

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Bioinformatics / n o&er&ie)

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Unit-1 Introduction to Bioinformatics

.ational /enter for iotechnology Information +./I defines

bioinformatics as a field of science in which biology, computer science,and information technology merge into a single discipline)

T,ere are 3 im"ortant sub-disci"#ines )it,inbioinformatics:

+i $e"elopment of new algorithms and statistics which assess relationshipsamong members of large data sets

+ii Analysis and interpretation of "arious types of data including nucleotideand amino acid sequences, protein domains and protein structures and

+iii$e"elopment and implementation of tools that enable access andmanagement of different types of information

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Unit-1 Introduction to Bioinformatics

A"ailability of 0$ structure of any biomolecule +eg) protein is "ital to

understand its structure ! function interactions )

%rimary structural +genomic or proteomic sequence data are obtainable

+experimentally in a faster and a more 1routine2 way

ut33)acquisition of 4$ and 0$ data, by experimental methods, is a

time*consuming and tedious tas#)

5herefore, theoretical structure prediction methods, employing

computational tools and algorithms, for prediction of 4$ and 0$

structures of biomolecules from their primary data, is an alternati"e

method, and one of the ma(or ob(ecti"e of bioinformatics +i) e)

molecular bioinformatics)

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Unit-1 Introduction to Bioinformatics

de&e#o"ments distin$uis, bioinformatics from c#assica#

bio#o$ica# and a##ied sciences

Integration of ad"anced physical techniques +lasers, better sequencers andmass spectrophotometer etc)

/entral role of computer*assisted operations in data acquisition and analysis+insilicobiological analysis)

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Unit-1 Introduction to Bioinformatics

""#ications

6nowledge*based drug design)

7orensic $.A analysis and agricultural biotechnology)

/omputational studies of protein*ligand interactions)

%ro"ide a rational basis for the rapid identification of no"el leads for synthetic

drugs)

6nowledge of the 0$ structures of proteins allows molecules to be designed

that are capable of binding to the receptor site +target protein with great

affinity and specificity)

""#ication and sco"e ofBioinformatics

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Unit-1 Introduction to Bioinformatics

$e"elopment of computational tools and databases, and

Application of these tools and databases in generating biological

#nowledge to better understand li"ing things)

Sco"e

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Unit-1 Introduction to Bioinformatics

Bioinformatics s(i## sets for a bio#o$ist

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Unit-1 Introduction to Bioinformatics

%attern disco"ery is one of the fundamental problems in bioinformatics)

8sed in multiple sequence alignment, protein structure and function

prediction, characterization of protein families, promoter signal detection

and other areas)

.ucleotide and protein sequences contain patterns or motifs that ha"e

been preser"ed through e"olution, because they are important to the

structure or function of the molecule)

2etectin$ "atterns in bio#o$ica#seuences

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Unit-1 Introduction to Bioinformatics

9ost common database which can be used for searching motifs andpatterns is %'-&I5)

%'-&I5 database : a compilation of motifs and patterns extracted fromprotein sequences and compiled by inspection of protein families)

&yntax of a %'-&I5 pattern consists of amino acid residues,interspersed with characters that denote the rules for the pattern, suchas distances between residues, and so on)

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Searc,in$ usin$ motifs and "atterns

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Codes used to define a 45OSITE "rotein "attern for a

searc, t,rou$, a seuence database

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%atterns can be generated from multiple sequences using %'A55

%atterns are described using the %'-&I5 syntax

%ower of %'A55 is that it requires no #nowledge of possible existingpatterns in a set of sequences

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45I!TS database

.ext generation pattern database consisting of fingerprints representingsets of conser"ed motifs that describe a protein family)

8sed to predict the occurrence of similar motif, either in an indi"idualsequence or in a database)

'efined by iterati"e scanning of the -;< composite sequence database:a composite, non*redundant database assembled from sources fromincluding &;I&& %'-5, sequences extracted from .'7 = %I' proteinsequence database, translated sequences from >enban# and the %$structural database)

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4ub#ic#% a&ai#ab#e soft)are too#s

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Summar%

ioinformatics includes application of computational tools and approaches to

the study of information content, organization, and processing in biologicalsystems)

9a(or impact on many areas of biotechnology and biomedical sciences) It hasapplications, for example, in drug design, forensic $.A analysis, agriculturalbiotechnology, etc)

%atterns of conser"ed sequences often highlight elements that are responsible

for structural similarity between proteins, and can be used to predict 0$structure of a protein)

5he %'-&I5 database is a compilation of motifs and patterns extracted fromprotein sequences and compiled by inspection of protein families)

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