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Course: MSC BT Semester: Iii Subject Code: MBT 305 Subject Name: Computational Biology Unit Number: 1 Unit Title: Introduction To Bioinformatics

This document provides an introduction to the unit on bioinformatics. It describes bioinformatics as the application of information technology to store, organize, and analyze biological data, especially nucleotide and amino acid sequences and protein structures. It discusses how detecting patterns in biological sequences is important for applications like multiple sequence alignment and protein structure prediction. It also introduces databases like PROSITE and PRINTS that contain conserved motifs and can be used to search for patterns.

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56 views

Course: MSC BT Semester: Iii Subject Code: MBT 305 Subject Name: Computational Biology Unit Number: 1 Unit Title: Introduction To Bioinformatics

This document provides an introduction to the unit on bioinformatics. It describes bioinformatics as the application of information technology to store, organize, and analyze biological data, especially nucleotide and amino acid sequences and protein structures. It discusses how detecting patterns in biological sequences is important for applications like multiple sequence alignment and protein structure prediction. It also introduces databases like PROSITE and PRINTS that contain conserved motifs and can be used to search for patterns.

Uploaded by

anirbanmanna88320
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PPT, PDF, TXT or read online on Scribd
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Unit-1 Introduction to Bioinformatics

Course

: MSc BT

Semester

: III

Subject Code

: MBT 305

Subject Name

: Computational Biology

Unit number

:1

Unit Title

: Introduction to Bioinformatics

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Unit-1 Introduction to Bioinformatics

Objectives
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

Lecture Outline

Introduction
Bioinformatics An overview

Bioinformatics skill sets for a biologist

Detecting Patterns in Biological Sequences


Summary

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Unit-1 Introduction to Bioinformatics

Introduction
Recall a famous quote by Harold Markowitz
regarding the relationship between computer
science and biology Computers are to
biology what mathematics is to physics.
Past few decades, major advances in the field
of molecular biology, coupled with advances in
genomic technologies led to an explosive
growth in the biological information generated
by the scientific community.
Surge of genomic information has led to an
absolute
requirement
for
computerized
databases to store, organize, and index the
data, and for specialized tools to view and
analyze the data

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Unit-1 Introduction to Bioinformatics

Bioinformatics An overview

Bioinformatics defined as the application of Information technology to


store, organize and analyze the vast amount of biological data available in the form of sequences and structures of proteins and
nucleic acids.

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Unit-1 Introduction to Bioinformatics

Bioinformatics An overview
Aims of bioinformatics

(i) Organization of data

(ii) Development of Analysis tool

(iii)Analysis of Data

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Unit-1 Introduction to Bioinformatics

National Center for Biotechnology Information (NCBI) defines


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

There are
bioinformatics:

important

sub-disciplines

within

(i) Development of new algorithms and statistics which assess relationships


among members of large data sets
(ii) Analysis and interpretation of various types of data including nucleotide
and amino acid sequences, protein domains and protein structures and
(iii)Development and implementation of tools that enable access and
management of different types of information

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Unit-1 Introduction to Bioinformatics

Availability of 3D structure of any biomolecule (eg. protein) is vital to


understand its structure function interactions .
Primary structural (genomic or proteomic sequence) data are obtainable
(experimentally) in a faster and a more routine way
But.acquisition of 2D and 3D data, by experimental methods, is a
time-consuming and tedious task.
Therefore, theoretical structure prediction methods, employing
computational tools and algorithms, for prediction of 2D and 3D
structures of biomolecules from their primary data, is an alternative
method, and one of the major objective of bioinformatics
(i. e.
molecular bioinformatics).
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Unit-1 Introduction to Bioinformatics

2 developments distinguish bioinformatics from classical


biological and allied sciences

Integration of advanced physical techniques (lasers, better sequencers and


mass spectrophotometer etc.)

Central role of computer-assisted operations in data acquisition and analysis


(in silico biological analysis).

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Unit-1 Introduction to Bioinformatics

Application and scope of


Bioinformatics
Applications

Knowledge-based drug design.

Forensic DNA analysis and agricultural biotechnology.

Computational studies of protein-ligand interactions.

Provide a rational basis for the rapid identification of novel leads for synthetic
drugs.

Knowledge of the 3D structures of proteins allows molecules to be designed


that are capable of binding to the receptor site (target protein) with great
affinity and specificity.

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Unit-1 Introduction to Bioinformatics

Scope

Development of computational tools and databases, and

Application of these tools and databases in generating biological


knowledge to better understand living things.

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Unit-1 Introduction to Bioinformatics

Bioinformatics skill sets for a biologist

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Unit-1 Introduction to Bioinformatics

Detecting patterns in biological


sequences

Pattern discovery is one of the fundamental problems in bioinformatics.

Used in multiple sequence alignment, protein structure and function


prediction, characterization of protein families, promoter signal detection
and other areas.

Nucleotide and protein sequences contain patterns or motifs that have


been preserved through evolution, because they are important to the
structure or function of the molecule.

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Unit-1 Introduction to Bioinformatics

Searching using motifs and patterns

Most common database which can be used for searching motifs and
patterns is PROSITE.

PROSITE database : a compilation of motifs and patterns extracted from


protein sequences and compiled by inspection of protein families.

Syntax of a PROSITE pattern consists of amino acid residues,


interspersed with characters that denote the rules for the pattern, such
as distances between residues, and so on.

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Unit-1 Introduction to Bioinformatics

Codes used to define a PROSITE protein pattern for a


search through a sequence database

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Unit-1 Introduction to Bioinformatics

Patterns can be generated from multiple sequences using PRATT

Patterns are described using the PROSITE syntax

Power of PRATT is that it requires no knowledge of possible existing


patterns in a set of sequences

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Unit-1 Introduction to Bioinformatics

PRINTS database

Next generation pattern database consisting of fingerprints representing


sets of conserved motifs that describe a protein family.

Used to predict the occurrence of similar motif, either in an individual


sequence or in a database.

Refined by iterative scanning of the OWL composite sequence database:


a composite, non-redundant database assembled from sources from
including SWISS PROT, sequences extracted from NBRF / PIR protein
sequence database, translated sequences from Genbank and the PDB
structural database.

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Unit-1 Introduction to Bioinformatics

Publicly available software tools

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Unit-1 Introduction to Bioinformatics

Summary

Bioinformatics includes application of computational tools and approaches to


the study of information content, organization, and processing in biological
systems.
Major impact on many areas of biotechnology and biomedical sciences. It has
applications, for example, in drug design, forensic DNA analysis, agricultural
biotechnology, etc.
Patterns of conserved sequences often highlight elements that are responsible
for structural similarity between proteins, and can be used to predict 3D
structure of a protein.
The PROSITE database is a compilation of motifs and patterns extracted from
protein sequences and compiled by inspection of protein families.

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