BIOINFORMATICS

Arushi
Dinesh
Kasi
Shruthi
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INTRODUCTION

• Bioinformatics has developed out of the need to understand the

code of life, DNA.

• Massive DNA sequencing projects have evolved and added in the

growth of the science of bioinformatics.

• The ultimate goal of bioinformatics is to uncover the wealth of

biological information hidden in the mass of sequence, structure,
literature and other biological data

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INTRODUCTION

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BIOINFORMATICS

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BIOINFORMATICS

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BIOINFORMATICS

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COMPONENTS OF BIOINFORMATICS

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WHAT IS DONE IN BIOINFORMATICS?

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WHY USE BIOINFORMATICS?

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APPLICATIONS OF BIOINFORMATICS
• Molecular medicine
 
• Personalized medicine
 
• Preventative medicine
 
• Gene therapy
 
• Drug development
  
• Microbial genome applications
  
• Waste cleanup
  
• Climate change Studies

• Alternative energy sources

• Biotechnology
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APPLICATIONS OF BIOINFORMATICS

• Antibiotic resistance
  
• Forensic analysis of microbes
  
• Bio-weapon creation
  
• Evolutionary studies
  
• Crop improvement
  
• Insect resistance
 
• Improve nutritional quality 
  
• Development of Drought resistance varieties
  
• Veterinary Science 
 
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SOFTWARE AND TOOLS

• Software tools for bioinformatics range from simple command-line

tools, to more complex graphical programs and standalone web-
services available from various bioinformatics companies or public
institutions.

• The computational biology tool best-known among biologists is

probably BLAST, an algorithm for determining the similarity of
arbitrary sequences against other sequences, possibly from
curated databases of protein or DNA sequences.

• BLAST is one of a number of generally available programs for

doing sequence alignment. The NCBI provides a popular web-
based implementation that searches their databases.

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BLAST

 Basic Local Alignment Search Tool.

 It is an algorithm for comparing biological sequences information,

such as amino acid sequence of different proteins or the nucleotides
of DNA sequences.

 BLAST is used to identify library sequences that resembles the

query sequences.

 The BLAST program was designed by Eugene Myers, Stephen

Altschul, Warren Gish, David J. Lipman and Webb Miller at the NIH
and was published in J. Mol. Biol. in 1990.

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BLAST

 BLAST is a tool for alignment of sequences.

Eg: To identify the unknown gene(query sequences) in the mouse,

the scientist will perform a BLAST search of the human genome
(library sequences) to see whether the human carrying the similar
gene or not.

 BLAST was originally developed by NCBI( National Center for

Biotechnology Information).

 Link: http://www.ncbi.nlm.nih.gov/BLAST/

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BLAST

 The NCBI site provides binary files for the following operating
systems and platforms.

 UNIX
 Linux
 Mac
 MS-Windows
 IBM AIX 5.1

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KINDS OF BLAST

 Nucleotide-nucleotide BLAST (blastn)

This program, given a DNA query, returns the most similar DNA
sequences from the DNA database that the user specifies.

 Protein-protein BLAST (blastp)

This program, given a protein query, returns the most similar protein
sequences from the protein database that the user specifies.

 Position-Specific Iterative BLAST (PSI-BLAST)

This program is used to find distant relatives of a protein.

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KINDS OF BLAST

 Nucleotide 6-frame translation-protein (blastx)

This program compares the six-frame conceptual translation products

of a nucleotide query sequence (both strands) against a protein
sequence database.

 Nucleotide 6-frame translation-nucleotide 6-frame translation

(tblastx)

This program is the slowest of the BLAST family.The purpose of tblastx

is to find very distant relationships between nucleotide sequences.

 Protein-nucleotide 6-frame translation (tblastn)

This program compares a protein query against the all six reading
frames of a nucleotide sequence database.

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PROCESS

 BLAST works through use of heuristic algorithm.

 Heuristic algorithm ,is an algorithm that is able to produce an

acceptable solution to a problem in many practical scenarios.

 Heuristics are typically used when there is no known method to

find an optimal solution ,under the given constraints.

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PROCESS

 Using a heuristic method ,BLAST finds homologous sequences,

not by comparing either sequences in its entirety, but rather by
locating short matches between the two sequences.

 This process of finding initial words is called seeding.

 While attempting to find homology in sequences, sets of

common letters, known as words.

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PROCESS

 For example:

 The sequences contain the following stretch of letters,GLKFA . If a

BLASTp was being conducted under default conditions,the word
size would be 3 letters.

 In this case, using the given stretch of letters, the searched words
would be GLK, LKF,KFA.

 The heuristic algorithm of BLAST locates all common words

between the sequences of interest (query) and the hit sequences
(sequences from database).

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USES OF BLAST

BLAST can be used for several purposes. These include:

 Identifying Species:
With the use of BLAST, you can possibly correctly identify a
species and/or find homologous species. This can be useful, for
example, when you are working with a DNA sequence from an
unknown species.
 Locating Domains:
When working with a protein sequence you can input it into
BLAST, to locate known domains within the sequence of interest.

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USES OF BLAST

 Establishing Phylogeny:
Using the results received through BLAST, you can create a
phylogenetic tree using the BLAST web-page.
 DNA Mapping:
When working with a known species, and looking to sequence a
gene at an unknown location, BLAST can compare the
chromosomal position of the sequence of interest, to relevant
sequences in the database(s).
 Comparison:
When working with genes, BLAST can locate common genes in two
related species, and can be used to map annotations from one
organism to another.

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SMITH-WATERMAN ALGORITHM

 The Smith-Waterman algorithm is a well-known algorithm for

performing local sequence alignment.

 This method varies from the BLAST method in two areas,

accuracy and speed. 

 A better alternative in order to find the best possible results.

 It is more time consuming.

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FASTA

 FASTA is a DNA and protein sequence alignment software

package.

 FASTA package contains programs for protein: protein,

DNA:DNA, protein : translated DNA , and ordered or unordered
peptide searches.

  A major focus of the package is the calculation of accurate

similarity statistics, so that biologists can judge whether an
alignment is likely to have occurred by chance.

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CONCLUSION

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