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BIF733 : Bioinformatics I (Essentials of Genome Informatics)

Course Overview

Course Synopsis

The course will provide basic knowledge to the beginners in bioinformatics. Mainly this course is designed to acquaint the students with bioinformatics, its methods and goals. The students would learn how bioinformatics differs from traditional biology and how traditional research methods can be improved using bioinformatics. What are modern day Genome Sequencing and analysis techniques and their applications? They will also be introduced with major Algorithms used for solving Biological problems.

Course Learning Outcomes

At the end of the course, you should be able to:

  • Recognize the importance of Bioinformatics in modern day research
  • What are main kinds of Biological data and how this data is stored into and retrieve from Biological databases?
  • Clear understanding of different types of Biological problems and major computational approaches to address these issue.
  • Have insights into Genomes and complexities of their analysis.
  • Relate the role of overlapping areas like Statistics and Mathematics in Bio-Computing
  • Explore modern day Genome sequencing technologies and the analysis of the high throughput data they generate.
  • Clear understanding of new requirements of Biologists (end users) and the approaches to find the most probable answers.

Course Calendar

Introducting Bioinformatics2PPTs
Scope of Bioinformatics3PPTs
Challenges in Bioinformatics4PPTs
Collaborating expertise5PPTs
Deoxy Ribose Nucleic Acid (DNA)6PPTs
Ribose Nucleic Acid (RNA)7PPTs
Central Dogma of Life9PPTs
Exceptions to Central Dogma10PPTs
Introduction to Bioinformatics Algrorithms11PPTs
Tasks mostly performed in Bioinformatics12PPTs
Introducing Algorithms13PPTs
Introducing Algorithms II14PPTs
Biological vs Computer Algorithms15PPTs
Types of Algorithms16PPTs
Approaches to design Algorithms17PPTs
Nucleotide Sequence databases18PPTs
Protein databases19PPTs
Genome and organism specific databases20PPTs
Gene expression databases21PPTs
Medical databases22PPTs
Sequence submission23PPTs
DNA Sequence Retrieval24PPTs
Protein Sequence Retrieval25PPTs
Sequence Formats26PPTs
Data Retrieval27PPTs
Genome Informatics28PPTs
Prokaryotic Genome29PPTs
Eukaryotic Genomes30PPTs
Assignment No. 1
Epichromosomal elements (EEs)31PPTs
Genome repeats32PPTs
Transposable Elements (TEs)33PPTs
Eukaryotic Gene Structure34PPTs
Comparative Genomics35PPTs
Comparative Proteomics36PPTs
Between proteome comparison37PPTs
Horizontal Gene Transfer38PPTs
Gene Order (Synteny)39PPTs
Genome annotations40PPTs
Genome Sequencing41PPTs
Developments for sequencing 142PPTs
Developments for sequencing 243PPTs
Cloning Techniques44PPTs
Sequencing Techniques45PPTs
Automated Sequencing46PPTs
ShotGun Sequencing47PPTs
HGP: Introduction48PPTs
HGP: Methods49PPTs
HGP: Outcomes50PPTs
Characteristics of Human genes51PPTs
HGP: Applications52PPTs
Next Generation sequencing (NGS)53PPTs
Exraction protocols54PPTs
Library Preparation55PPTs
NGS Platforms57PPTs
454 Pyrosequencing58PPTs
Illumina Sequencing59PPTs
Ion Semiconductor Sequencing60PPTs
Assignment No. 2
3rd Generation Sequencing61PPTs
Helicose Sequencing62PPTs
Pacbio Sequencing63PPTs
Oxford Nanopore Sequencing64PPTs
Comparison of NGS methods65PPTs
Scope of NGS66PPTs
Applications of NGS67PPTs
Genome Sequencing68PPTs
Transcriptome Sequencing69PPTs
Epigenome Sequencing70PPTs
Metagenome sequencing71PPTs
Five Big Projects in NGS72PPTs
NGS Output Formats73PPTs
NGS Quality Scores74PPTs
NGS Data Quality Control75PPTs
NGS Data Analysis76PPTs
Galaxy: Tools78PPTs
NGS: Mapping and Visualization79PPTs
Genome Assembly80PPTs
Genome Assembly Overview81PPTs
Genome Assembly Planning82PPTs
Effect of Repeats83PPTs
Related species Assembled84PPTs
Greedy Graph Algorithm85PPTs
Lander Waterman Curve87PPTs
Assembly Pipeline188PPTs
Assembly Pipeline289PPTs
Quality of Assembled Genome90PPTs
Overlap Layout Consensus92PPTs
De Bruijn Graph93PPTs
De Bruijn Graph Example94PPTs
Assembly Issues95PPTs
Introduction to Statistics96PPTs
Measure of Central Tendency99PPTs
Data Presentation100PPTs
Mid Term Examinations
Box plot101PPTs
Mutually Exclusive Events103PPTs
Union and Intersections104PPTs
Types of Probabilities105PPTs
Bayes Theorem106PPTs
Occasionally dishonest casino107PPTs
Maximum Likelihood Estimation108PPTs
Binomial Distribution109PPTs
Normal Distribution110PPTs
Markov Chains111PPTs
Probabilities in Markov Models112PPTs
Markov Chain Model113PPTs
Occasionally Dishonest Casino 2115PPTs
Defining Genes116PPTs
Finding Genes117PPTs
Gene Prediction118PPTs
ORF Prediction119PPTs
ORF Finders120PPTs
TSS Prediction121PPTs
Prediction of Splice Junctions122PPTs
Prediction of Exons123PPTs
Annotation of assembeled Genome124PPTs
Pattern Finding in a Genome125PPTs
Pattern Finding Algorithms126PPTs
Assignment No. 3
Brute Force Approach127PPTs
Knuth-Morris-Pratt Algorithm128PPTs
KMP: Prefix function129PPTs
KMP: Execution130PPTs
Boyer Moore Algorithm131PPTs
Pair Sequence Alignment132PPTs
Scoring Schemes133PPTs
Subsitution Matrices134PPTs
Needleman-Wunsch Algorithm136PPTs
Needleman-Wunsch Execution137PPTs
Smith-Waterman Algorithm138PPTs
Dynamic programming: Complex Models139PPTs
FASTA Algorithm141PPTs
Doing BLAST locally143PPTs
P Value144PPTs
Significance of Scores145PPTs
Extreme value Distribution (EVD)146PPTs
Hidden Markov Model (HMM)147PPTs
HMM: Generating Sequences148PPTs
HMM: Classical problem149PPTs
HMM: Viterbi Algorithm150PPTs
HMM: Viterbi Example151PPTs
HMM Example Casino Revisited152PPTs
Multiple Sequence Alignment153PPTs
Steps of Multiple Sequence Alignmemt154PPTs
MSA: Approaches155PPTs
Dynamic Programming156PPTs
MSA Algorithm157PPTs
MSA: Scoring158PPTs
MSA: Progressive Method159PPTs
MSA: Iterative Methods160PPTs
Simulated Annealing161PPTs
Assignment No. 4
Assessing Quality of MSA163PPTs
Phylogenetic Analysis166PPTs
Phylogenetic Analysis and MSA167PPTs
Evolutionary Tree168PPTs
Moleculer Phylogenetics169PPTs
Tree Reconstruction Methods170PPTs
Maximum Parsimony Method171PPTs
Maximum Likelihood Method172PPTs
Distance Matrix173PPTs
Fitch Morgolish Algorithm175PPTs
Neighbor Joining Method176PPTs
RNA Structure177PPTs
RNA Secondary Structure178PPTs
RNA Secondary Structure Prediction179PPTs
Base Pair Maximization180PPTs
Nussinov Algorithm181PPTs
Transformational Grammars182PPTs
Microarray Types184PPTs
Array Design185PPTs
Array Applications186PPTs
Experimental Design187PPTs
Microarray Image Processing188PPTs
Microarray Normalization189PPTs
Within Array Normalization190PPTs
Between Array Normalization191PPTs
RNASeq Normalization193PPTs
Data Analysis194PPTs
t distribution195PPTs
t Test Example196PPTs
Two sample t Test197PPTs
Paired t Test198PPTs
Multiplicity Issue199PPTs
GO functional Analysis200PPTs
Gene Networks201PPTs
Final Term Examinations
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