Introduction To Bioinformatics Presentation

INTRODUCTION TO BIOINFORMATICS
Group Members
1. Namuhubembe Melisa Grace
2. Odong Sam
3. Lomokol Jonathan
4. Ntanda Rashid
5. Aheirwe Norbert
PRESENTATION CONTENT
Overview of the Human Genome

Bioinformatics; An interdisciplinary field
Sequence Alignment
Pairwise Sequence Alignment
Dynamic Programming
Global Alignment
Local Alignment and BLAST
Other Bioinformatics Tools and Resources
Bioinformatics Databases
Next Generation Sequencing
OVERVIEW OF THE HUMAN GENOME
• The human genome, consisting of approximately 3.1 billion base pairs,

serves as the instruction manual for life.
• It is composed of four nucleotides: Adenine (A), Thymine (T), Cytosine (C),
and Guanine (G).
• Around 2.9% of the genome comprises genes responsible for encoding
proteins.
• These seemingly simple sequences hold the key to unraveling the mysteries
of life and understanding evolutionary processes.
• Bioinformatics plays a crucial role in sequencing and analyzing genomes of
various organisms.
BIOINFORMATICS: AN INTERDISCIPLINARY FIELD
• Bioinformatics is an interdisciplinary field that combines

biology, computer science, and statistics.
• It involves the development and application of computational

tools and techniques to solve biological problems.
• Numerous online bioinformatics tools, with user-friendly

interfaces and tutorials, are freely available to biologists.
• However, it is essential to grasp the underlying principles of

these tools to utilize them effectively.
• Understanding the assumptions and methodologies behind

the tools ensures accurate analysis and interpretation.
SEQUENCE ALIGNMENT
• Sequence alignment is a fundamental technique for comparing and identifying similarities

between DNA or protein sequences.
• It is used to determine the alignment between two given sequences (S1 and S2).
• The similarity between amino acids in the sequences is assessed using a substitution
matrix, such as BLOSUM62.
• The goal is to find the optimal alignment that maximizes the scoring function, which
quantifies the quality of alignment.
• Traditional enumeration-based methods are theoretically feasible but impractical for

large-scale applications, necessitating faster algorithms.
PAIRWISE SEQUENCE ALIGNMENT
• Pairwise sequence alignment is a specific type of sequence alignment

used to align two given sequences.
• It is used to compare and identify similarities between sequences, such as

DNA or protein sequences.
• The alignment process considers the similarity between amino acids in the
sequences using a substitution matrix.
• The optimal alignment is determined by maximizing the scoring function,

which quantifies the quality of alignment.
• Dynamic programming algorithms, such as the Needleman-Wunsch

algorithm, are commonly used for pairwise sequence alignment.
DYNAMIC PROGRAMMING
• Dynamic programming is a problem-solving technique used in various fields, including

bioinformatics.
• It solves complex problems by breaking them down into smaller overlapping subproblems.
• The solution to each subproblem is stored and reused to solve larger subproblems, leading to an
optimal solution.
• In sequence alignment, dynamic programming is used to find the optimal alignment by iteratively
filling a matrix.
• The Needleman-Wunsch algorithm, based on dynamic programming, efficiently performs global

sequence alignment.
GLOBAL ALIGNMENT
• Global Sequence Alignment is a type of sequence alignment

that aligns two sequences along their entire length.
• It is used to align closely related sequences, such as

homologous genes or proteins with similar functions.
• The Needleman-Wunsch algorithm is a widely used

algorithm for global sequence alignment.
• The algorithm considers user-defined scoring functions and

uses dynamic programming principles.
• It identifies regions of similarity and produces an alignment

that maximizes the overall score.
LOCAL ALIGNMENT AND BLAST
• Local Sequence Alignment is used to identify short, similar

regions between two sequences.
• The algorithm, such as the Smith-Waterman algorithm, detects

significant local alignments.
• Basic Local Alignment Search Tool (BLAST) is a widely used

bioinformatics tool for local alignment searches.
• BLAST employs heuristics and indexing techniques to

efficiently search large databases for similar sequences.
• It provides valuable insights into evolutionary relationships,

functional annotations, and protein structure predictions.
OTHER BIOINFORMATICS TOOLS AND RESOURCES
• Multiple sequence alignment tools, such as Clustal Omega and

MUSCLE, align three or more sequences simultaneously.
• Phylogenetic analysis tools, like PhyML and MrBayes,

reconstruct evolutionary relationships based on sequence data.
• Structure prediction tools, including I-TASSER and SWISS-

MODEL, predict the 3D structure of proteins.
• Functional annotation tools, such as DAVID and PANTHER,

provide functional information about genes and proteins.
• Data visualization tools, such as R and Python libraries,

facilitate data exploration and presentation.
BIOINFORMATICS DATABASES
• Bioinformatics databases store, organize, and provide access to

vast amounts of biological data for research and analysis.
• These databases contain diverse information, including DNA and

protein sequences, gene expression data, metabolic pathways, and
genetic variations.
• Integration of data from multiple sources enables comprehensive

analyses
NEXT GENERATION SEQUENCING (NGS)
• Next Generation Sequencing (NGS) technologies have

revolutionized DNA sequencing by generating a vast amount of data.
• Over 1000 NGS sequencers are available worldwide, surpassing the

capabilities of the Sanger sequencing method.
• NGS, also known as deep sequencing, produces shorter reads with

higher error rates compared to traditional methods.
• NGS has facilitated research in genomic DNA sequencing,

epigenetic modifications, transcriptomes, and protein-DNA
interactions.
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INTRODUCTION TO BIOINFORMATICS

Overview of the Human Genome

• The human genome, consisting of approximately 3.1 billion base pairs,

• Bioinformatics is an interdisciplinary field that combines

• It involves the development and application of computational

• Numerous online bioinformatics tools, with user-friendly

• However, it is essential to grasp the underlying principles of

• Understanding the assumptions and methodologies behind

• Sequence alignment is a fundamental technique for comparing and identifying similarities

• Traditional enumeration-based methods are theoretically feasible but impractical for

• Pairwise sequence alignment is a specific type of sequence alignment

• It is used to compare and identify similarities between sequences, such as

• The optimal alignment is determined by maximizing the scoring function,

• Dynamic programming algorithms, such as the Needleman-Wunsch

• Dynamic programming is a problem-solving technique used in various fields, including

• The Needleman-Wunsch algorithm, based on dynamic programming, efficiently performs global

• Global Sequence Alignment is a type of sequence alignment

• It is used to align closely related sequences, such as

• The Needleman-Wunsch algorithm is a widely used

• The algorithm considers user-defined scoring functions and

• It identifies regions of similarity and produces an alignment

• Local Sequence Alignment is used to identify short, similar

• The algorithm, such as the Smith-Waterman algorithm, detects

• Basic Local Alignment Search Tool (BLAST) is a widely used

• BLAST employs heuristics and indexing techniques to

• It provides valuable insights into evolutionary relationships,

• Multiple sequence alignment tools, such as Clustal Omega and

• Phylogenetic analysis tools, like PhyML and MrBayes,

• Structure prediction tools, including I-TASSER and SWISS-

• Functional annotation tools, such as DAVID and PANTHER,

• Data visualization tools, such as R and Python libraries,

• Bioinformatics databases store, organize, and provide access to

• These databases contain diverse information, including DNA and

• Integration of data from multiple sources enables comprehensive

• Next Generation Sequencing (NGS) technologies have

• Over 1000 NGS sequencers are available worldwide, surpassing the

• NGS, also known as deep sequencing, produces shorter reads with

• NGS has facilitated research in genomic DNA sequencing,

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